My personal thoughts:
1. General caster/melee imbalance.
Pathfinder response: make the problem worse (they nerf power attack, one of the few things that meleers had going for them and buff wizards)
False. A melee combatant has appreciably more options for putting the hurt down on a caster that gets anywhere near here. The 5' step away defense and casting defensively are no longer the sure thing they used to be. If a fighter is built right, casters should be very afraid.
2. Saving throw DC scaling faster than bonuses to saves since its easier to boost one number (the DC) than three numbers (three kinds of saves).
Pathfinder response: make the problem worse (easier to get mental stat bonuses, etc.)
The only save or suck spells (without repeat saves,) left are fort saves, so your melee people will be strong against that. From my initial purview the only save or suck spells left of this type are flesh to stone and baleful polymorph.
As for raising DCs easier than raising saves, let's look at the numbers.
Using baleful polymorph:
DC = 10+5(spell level)+5(int assuming base 18)+spell focus, greater spell focus= 22
Save bonus: d20 + 7 +3(16 con) +2 (great fortitude)= d20+ 12. You need to roll a 10, so it's a 55% chance of saving.
Now that's not the end of it. If I give the wizard (with fewer feats) two feats towards this effort, why not give it to the fighter? He'll get Improved Great Fortitude where he gets to re-roll the fort save if he wants once a day. That makes his chance of failure: (.45^2)= 20% chance of failing both.
If we take into account magic items towards the cause the wizard can add in an intelligence boosting item. Say for this level it's a +4(being nice). On the fighter's side, he's got two magic items to counter it with, both a stat boosting item and a resistance item (and resistance items are cheap). Since they now make the items take the same slot and you get a discount for stacking effects, the fighter might well have a +2 str/con belt. Add in a nice cheap +2 cloak of resistance, and the fighter still mostly shrugs off this attack. These two items (Belt of physical might +2 10k and cloak of resistance +2 4k) come to less than the stat booster of the wizard (Headband of Vast Intelligence +4 16k).
3. Too many little fiddly things to keep track of.
Pathfinder response: make the problem worse (too many round/day effects).
Huh? I don't see anything but a wash here.
4. The way the multiclassing works certain cool combinations just don't work unless you jump through a whole lot of PrC hoops
Pathfinder response: make the problem worse by nerfing multiclassing in general thereby making fighter/wizards even weaker than before (and I always loved playing them in 2ed ). This one is somewhat forgivable since it would require overhauling 3.5ed multiclassing to fix.
The continued lament of people hearkening back to the brokenly overpowered dual casters of 2nd Edition does nothing but make me laugh in derision.
As for the claim that they nerfed multiclassing compared to 3.5, sorry I don't see it. While they did make single classes better for those that stick with them, this isn't a problem considering how many classes ended up being dip classes in 3.5.
5. 15 minute adventuring days.
Pathfinder response: no change.
More abilities which can be used a bunch of times in a day, more healing, and bonded items say you are wrong. Now granted some moron can still go nova in a single encounter, but resource management has always been a factor in playing D&D correctly. If your people didn't figure that out, the game is not to blame.
6. Magic item Christmas Tree effect.
Pathfinder response: make the problem worse by making magic item creation easier.
From what I recall the wealth per level is less in Pathfinder which puts a damper on the magic item business, and they changed magic item availability. No longer is pretty much anything you want available at K-Magic. There's only a chance that things will be there, and making stuff yourself eats plenty of time and money.
7. Lots of classes just don't have enough skill points for things it makes sense for them to do.
Pathfinder response: small improvement because of merging skills and changing how cross class skills worked. But come on, would it have killed you to give the fighter 4 skill points?
The skill consolidation is a huge change, and with favored class, that 2 goes to a 3 if you care about skills.
8. Druid animal companions can often out melee a lot of melee characters ("my class feature is more powerful than your entire class!")
Pathfinder response: moderate move in the right direction, but the druid is still quite rather overpowered.
I question this. They smacked the druid pretty hard with the nerf bat.
9. A lot of the really cool splatbook classes I want to play are a lot weaker than their closest core equivalent (poor swashbuckler and warlocks, I weep for you).
Pathfinder response: make the problem worse by increasing the power of the Core classes so that they overshadow the splatbook classes even more.
Tough noogies. They can't be responsible for material they aren't even allowed to cite (closed content)
10. Combat is often pretty boring with the same one trick ponies using their tricks over and over again.
Pathfinder response: I haven't read the rules enough, but I'm not seeing that big of a change here, that said I can probably forgive this one since this would be hard to do without really overhauling 3.5ed in a big way.
Everyone got tons more feats, most classes got a bunch more special abilities. You aren't bothering to look.