Some comments on your suggestions:

A fast to open or close hatch (like Apollo or even faster) if only for safety reason.

That should be a given. The reason why the Apollo 1 crew couldn't open their hatch is that it was designed to open inwards. This design is lighter because the internal pressure pushes the hatch against the seals. However, when the fire started, the internal pressure instantly became very high. It wasn't humanly possible for anyone to open the hatch under those conditions. For subsequent Apollo capsules, the hatch was designed to open outwards. This improved safety at the expense of weight, but it was a worthwhile tradeoff.

A sea level atmospheric pressure (if there had been a fire in a MIR in pure oxygen, all 6 astronauts would perhaps not haver survived it in 97) with a shirtsleeve environment for going up and coming down (perhaps a pressure suit like the Russian Sokol but not like the Shuttle astronauts).

Nothing is free in spacecraft. A sea level atmospheric pressure means the capsule has to be stronger, therefore heavier. Having nitrogen in the atmosphere is good except for during an emergency where the cabin pressure is dropping. If pressure drops quickly, the nitrogen can give the crew the bends which would hamper their ability to get into their spacesuits.

Pure O2 is of course dangerous, but it was especially so in the case of Apollo 1. The Apollo cabin pressure was something like 5 PSI differential with a pure O2 atmosphere. To get that, they pressurized the capsule to 5 PSI greater than ambient, so the actual pressure was almost 20 PSI. It was an accident waiting to happen. The fact that they'd done the same thing with the Mercury and Gemini missions just meant they'd been lucky.

Ingressing the capsule before liftoff at a later moment in the countdown, not forcing the astronauts to lie down too long.

This also is a tradeoff. Is it safer to board the spacecraft before or after it is fueled? If you have a launch escape system, then boarding before final fueling might be safer because you can get away at any time. In addition to the crew's safety, you have to consider the pad personnel. It's a dangerous enough job.

There's also the question about how long the pre-takeoff checklist is. Common NASA practice (at least up through Apollo) is to have the backup crew preposition many of the switches so the prime crew doesn't have so much to worry about. However, there are always checklist items that can't happen until specific times in the launch sequence.

A shroud hard enough and a rocket strong enough to withstand all kinds of weather paterns (temperature variations, rain, winds, etc..) at liftoff. Of course, a storm should better be avoided.

Again, the issue is added weight. All rockets are designed to handle a certain range of conditions such as wind shear at different altitudes and launch temperatures. You can design the vehicle to handle stronger winds but that comes at the expense of payload. All aerospace vehicles are a series of compromises flying in close formation. Rockets are no exception. Many of the Soviet-era launchers were derived from ICBMs where the ability to launch in all sorts of weather conditions was a priority. A booster designed for civilian launches from Florida doesn't have to be built to survive severe winter conditions like those found at Russian launch sites.

Easy and quick docking and undocking procedures; a spacesuit that's not too hard to get into and out of.

This shouldn't be too difficult to manage.

For landing, capabilities to land on the ground or on water.

Early American spacecraft were designed to land on water as a first option but they could also hit land. It would've roughed up the crew but they would've survived. If they go with parachutes, then perhaps we should adopt the landing retrorocket system that the Russians have used for so long. They also use it when airdropping heavy equipment. The system is simple and appears to be reliable. Of course, it's one more thing that could fail with potentially disasterous results (e.g. premature firing would probably destroy the parachute). If they go with a CRV style parafoil, then retrorockets wouldn't be necessary.

Each time the Shuttle lands, it takes an hour for astronauts to get out of the vehicle! What if there were some kind of emergency?
The next spacecraft should make it possible to get out from only seconds after landing.

One of the reasons why it takes so long for the Shuttle crew to disembark (I don't think the delay is actually an hour) is that there may be residual hypergolic propellant fumes from the reaction control system thrusters. Those fumes are highly toxic and corrosive. You may have noticed a vehicle with a windmill looking contraption on it parked near the Shuttle after landing. That's a large fan to blow away any fumes. There may also be heat issues to contend with. The Shuttle gets pretty hot during reentry and may need some time to cool. Even the SR-71 had to contend with this issue. They'd either circle around at subsonic speeds or do some touch-n-goes to give the plane time to cool. One crew didn't do that before landing at Okinawa and had to wait quite a while before they could get out.

Of course, in an emergency, they'd get out quickly even from the Shuttle.