1. I prefer ammo to overheating primarily due to the overload issue in ME 1. ME 2 wins here.
2. I would have to say that I do like the new upgrade and weapon finding system over the old system because there were too many guns to buy, upgrade and keep track of. In the time period they're talking about gun replication would easily be possible so if you had one really good gun why couldn't you make copies of it and give it to the rest of your squad members?
Finding a bunch of useless guns and having to sell them is a system for loot-based games like Borderlands and just doesn't work in ME.
3. The skills were certainly more varied in ME 1, but at least now you don't have to spend points on charm / intimidate, you can just act how you want. You can also respec your character at any time. ME 2 wins here as well. (Also, love the new biotic power combos, Adept is the best class to play, bar none!).
4. I will agree with your points here... the mini games in ME 1 were better and at least skippable.
5. While I had no problem with the elevator rides and loading, the new system breaks immersion too much. Especially the mission summary screen. ME 1 wins here as well.
6. Driving the mako around looking for shit on planet surfaces was really only hampered by the rough terrain on planets and having to fight in the mako. I spent so much omni-gel fixing the damn thing. I'm glad they got rid of that part. I like the unique landscapes presented in ME 2, even if it doesn't feel as much like exploring and more like new levels.
7. I liked the exploring in ME 2 and it had a purpose. Finding the signals on planets and investigating not only opens up other planets and options but it also earns you experience. ME 2 wins here big time, though I do wish there were at least something to collect for the completionists out there. Investigating the crash of the original Normandy just wasn't enough for me.
Overall, I think ME 2 is better than ME 1, but there are things from ME 1 they definitely should have kept in

.