I'll answer your questions first then make a long statement that gives the basis for many of my conclusions.

1)I'm an electrical/computer/software/systems engineer which has less relevance than I'm an experienced sifter of information who has followed general technological advances and our space program since its inception. I've been part of the Moore's law computer age dreaming up how to have current generation computers/software help us design next generation computers/software.

2) Certainly Mars is much more amenable to long term colonization than the Moon.

3) This is a key assumption I disagree with strongly. A small moon habitat built with robots could not possibly be anywhere on the same cost scale as a sustainable Mars colony. Communication and teleoperation will be much easier and the scale of the habitation could be much smaller. Unless access to water is found, I wouldn't bother to think about putting men there as well. The 3 main objectives I would have for the moon would be:
a) is there accessible water there or not
b) could I figure out a way to make cheap power stations on the moon(in situ solar cell manufacture)
c) could I figure out a way to make lunar resources available for near earth space infrasture usage. (thus potentially making such projects as Mars colonization cheaper).

4) The science program works just fine, by prioritizing science objectives within the scope of answering certain visionary question (e.g. is there life in the solar system). I believe a manned space program could work just fine, by breaking up the visionary task of enabling sustained manned presence off planet into more definable(and tractable) minor goals (like health effects of low gravity and methods to mitigate them).

5) A heavy lift vehicle (or anything that will lower the cost to get payload out of orbit) is a basic enabling technology. A manned rated heavy lift vehicle will not be necessary until we've answered a lot of questions and built up a lot of space infrastructure. I don't agree that manning missions to mars will speed our answers about life on the Mars. A more aggressive robotic probe program would do that a lot more cheaply. I do agree with some of your thoughts about commercialization of space and go into it in more detail below
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OK, I've answered your questions now for some background and conclusions:

1) Governement funded big science is more often than not a disaster. Basically, the bigger the project, the costs multiply higher, the delays are longer, and the results are iffy at best (often canceled or reduced vision).

Some non-space examples:

Star Wars--a brilliant political objective but premature technologically and thus a huge waste of (investment) money. It was brilliant politically because the public would not pay for any more offensive weapons since we had overbuilt missiles by orders of magnitudes, but evidently they could be scared into spending billions for defensive vapor ware.

SSC--spent 2 billion before costs ballooned to $12B and it was cancelled.
LHC--taken double the money and twice the time and still not working
ITER(fusion)--another huge large project money waster--when will this ever operate?
NIF(laser)--at least this has been completed (for multiples of original budget and time to build)
Manhattan project (a success, which I largely credit to wartime focus, and by relative scale to modern large projects not all that big and complex).

Let's look at some of NASA space history:

Apollo--we spent a massive amount of money, and used the very best minds of the country for a decade. The result was a handful of missions to the moon with no sustainable technology path as a legacy. This was a political success, an engineering success, but not a sustainable programatic success.

Spaceplanes--how much money down the rathole to fund canceled projects with only the shuttle being built. And the shuttle has never met its design goals for cost and reuse.

ISS--massive white elephant. 100 Billion dollars later and it is still being built with practically no science done and lives lost. This is an example of manned space as a jobs program with no real goals other than to give a reason for the shuttle to operate.
(p.s.) I was extremely angry when the first module was (rushed) to launch to avoid cancelation because of delays--proper management would have canceled this program and started work on next generation launch vehicle (beyond the shuttle) instead. By going this path we've wasted 200B and set back the space program decades.

The ISS is very relevant to current off world base plans. These are huge projects with no real sustainable objectives, and lack of understanding of detailed engineering requirements, and no reason to make budget (once launched very difficult to cancel aerospace jobs programs).

Robotic probes--much more cost effective (and obviously pose 0 risk to humans). The science return of NASA probes has been enormous (mapping and exploring entire planets from orbit, and some sporadic ground truth landers and rovers). Just the fact they don't have to come back probably reduces cost an order of magnitude. The recent management failures related to the MSL illustrates the dangers of losing control of a project as more complexity is added. Now imagine scaling this up to a manned effort (predictable disaster with current state of technology).

Future Space:
If some project is stated that it will cost $150B then by the law of diminishing returns of big govt projects it will be $1Trillion to do a less modest version than the original version. This is the scale we're talking about for manned expeditions to other worlds. We need to do the groundwork that will lower the costs and the unknowns to levels that can be conceivably handled by the govt (or even better will be undertaken privately.)
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2) Currently, exploration in hostile environments is better(more cost efficiently) done by machine extensions of ourselves(robotic probes). Virtually all our knowledge of the solar system has not come from personal visits. Robotic probes are getting significantly better and cheaper. Witness the age of the UAV, and USV (unmanned air and sea vehicles). Non-profit ventures (like NASA) should do their exploration and survey work with robotic probes and rovers. The focus should be science return to understand our universe and laying the groundwork for sustained presence off planet.

3) Current plans for manned exploration of mars and space bases on the moon are emotionally and politically based and have little value beyond a vision. I say this because basic knowledge necessary to make such plans is missing. See 2) for the cheapest way to find the basic knowledge necessary to make the plans.

4) The most effective science and exploration and in general human advancement is usually based on allowing a natural evolution of the use of technological advancements. We've entered the robotic age, and yearly robotic capabilities get demonstrably better. Virtual control and communication for teleoperation is also improving by leaps and bounds. 3D technology will permeate society over the next decade, and virtual presence will become immensely better and cheaper. All of these advances should point to heavier use of robots for solar system exploration (not men).

5) Given the previous understandings, manned space should be about tourism, media, and ultimately colonization, NOT EXPLORATION. Currently the most viable avenue to off planet manned presence in through private companies not NASA. Private companies will not disconnect from (for profit) budget considerations. Thus a true bootstrapping process will occur, with natural technology advances happening to enable less expensive trips off planet. I am watching Bigelow enterprises with great interest, because most important manned space event since apollo would be a private trip to a private space hotel. Cheap inflatable habitats could be on the true road to extended space tourism and colonization. I believe tourist trips to a Moon hotel are much more likely to take the first private citizens to another world than a Mars trip.

Private companies ability to sell media rights could very well be the tipping point for a viable manned space market. How much could you sell the rights to shoot the first movies using a real space environment? Just as one more example of the NASA disconnect from markets is the fact that NASA media is for public consumption (as it is publicly funded).

6) NASA could be an enabler of private space enterprises and ultimately colonization. This is actually the role I would prefer. As I've stated before, I think a key mission NASA could fulfill is low gravity research. We need to definitively find out the effects of not just 0G but all levels from 0 to earth, especially Mars and Lunar.

Another key mission of NASA should be preliminary surveying and prospecting to understand offworld environments and resources. NASA should contract to private space companies whenever possible (if they can get astronauts cheaper to the ISS than NASA so be it, use them).

Since I don't believe in non-profit visiting, NASA should also work on enabling technologies to lower costs of sustainable colonization. This will be largely roboticized off world exploitation of materials. It would also include building up whatever space infrastructure makes sense to ultimately to lower costs of its goals (e.g. heavy lift cargo vehicle, space fueling station?).
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In conclusion I would like NASA to safeguard its science budget, by fixing the budget of its manned space element. The manned space element needs completely new leadership with the focus on long term enabling of colonization and private space development.

When and if they develop the technology to do manned Mars missions for 5B and 5 years, I might be able to get behind it. But I really think our manned destiny off world will and should be in private hands.