"Except possibly that there was a sizeable resistance to AQ/Taliban in Afghanistan.
There was no armed resistance to the regime in Iraq."

Kurds.

The Kurds were supported by Bush I and throughout Clinton administration and into Bush II.
Also, Saddam attack and slaughtered people in Basra area and many were forced to flee to Iran.
One could roughly say the Kurds got western help and Southern Iraq got Iranian help- the southern Iraq basically lost, and northern Iraq achieved indepedence [though not formal recognition of independence] from Saddam's rule. Though the smale scale fighting/covert operations never stopped [in either the south or the north] until the Coalition forces invaded Iraq and removed Saddam from power.

"Granted, those Afghans are a bunch of bloodthirsty warlords intent on gaining power, but at least they're nominally on our side."

Nominally? We provided air support and ground coordination to air- mainly. No significant number US tanks or armored vehicles as far as I know.
If you mean by nominally, that they weren't directly commanded by the US miltary, but were instead independent allied forces, I would agree.

"Now, given the troops, money and other resources that have gone into Iraq since 2003, would Afghanistan be in better shape than it is today?"

It's unlikely that Afghanistan would have recieved more support, if not for Iraq war. And it's unlikely that we would have as much international involvement in Afghanistan without the Iraq war. Canada and France can say we don't support Iraq war BUT we do support the war against Terrorism and efforts in Afghanistan- and here is the troops that prove it. Canadian involvement in terms of ground forces and naval assets is very significant considering it's total miltary capablity- and is significant even compared the US forces in term of effort regarding Afghanistan.