1. The rift between warrior-types and caster-types is wider. Yes, that’s right. The primary source of imbalance in the rules – the fact that different sets of the core classes are drastically more or less powerful than others – is worse now. Several of the core player races now have ability score bonuses that actually increase their DCs. Also, casters get more feats just like the warrior-types get. And their feats weren’t made worse by the transition. The two trip feats that warrior-types can get are not as good as Improved Trip from the core, and they don’t get twice as many feats. This is further accentuated by the change to Power Attack, a source of big damage for the warrior in 3.5. There, one could use Shock Trooper or tripping to make the penalty from Power Attack hurt less and get similar damage from the penalty taken. In Pathfinder, not only can you not get similar bonuses in damage, but you can't even decide by how much you power attack.
Another way that warrior-types were totally castrated is the Stand Still feat which was basically the only way much of the time to stop large enemies that were unfeasible to trip from getting to the squishies, allowing warriors to actually act as a tank. Contrasting the old and new versions, we can see that the new one is almost completely ineffective. First, it completely neutralizes the whole point of having a reach weapon, since it only allows one to affect enemies who are adjacent to the tank, and you have to make a CMB check against the foe, which is often impossible (see #2 for more info). Beyond just hitting things for damage that's barely decent, warriors in Pathfinder have no way now of forcing enemies to deal with them, allowing enemies to wander unhindered past fighters and towards the squishies, leaving fighters little to do but run after them, hoping to get another hit or two in.
2. Fighters still don’t get nice things. At most, Pathfinder has stalled the point at which Fighters go obsolete by one or two levels. The things they get are still bounded heavily by what already existed and the lack of designers’ imagination and understanding. Monks are still unable to actually hit incorporeal things until they get an Amulet of Mighty Fists (which is actually able to give the nice weapon properties; there are things worth keeping from Pathfinder, much like pearls in a pile of sludge). Oh, and while the Bracers of Armor do give unarmored people the nice armor properties, you need to enhance them up to +4 armor or they shut down the moment someone casts mage armor on you. And although there are more feats per character, fighters still get the same number from class levels, and the feats are individually worse. Even worse is that monsters can still bust out the same tricks that they did before; the cockatrice (for example)
This is made even more visible by the differences between the CMB of many meleers and the CMD of monsters. Opening up the Pathfinder Bestiary, we notice creatures like the Ankheg, a CR 3 creature with a CMD of 25 against trip attacks--which are incidentally the fighter-type's primary form of stopping enemies from getting away from them. Or the Dire Crocodile, a CR 9 creature that has a CMD of 40 against trips, where a level 9 fighter might have a CMB of +16 (5 (Strength - 16 (Base) + 2 (level) + 2 (item) + 9 (BAB) + 2 (Magic Sword)). Even with both trip feats, the fighter has a 5% chance of tripping the crocodile. The tyrannosaurus, at the same CR, has one less CMD--but against all attacks, not just trips. Meanwhile, monsters still have most, if not all their old tricks. Meleers can do very little against a Nalfeshnee who can still use Greater Teleport at will, along with Greater Dispel Magic, Call Lightning, and Feeblemind--all also at will.
Another example of this is the DC change to traps. Now the acid arrow trap (CR 3) has a DC of 27--both to perceive and disarm. What kind of rogue is going to be able to make that kind of check? Rather than trapfinders, rogues have become glorified barbarians--but without the HP needed to buffer against the injury some of the traps inflict.
Some might say that selectively nerfing specific spells balances this out, but when battles take on average three rounds, spells like Glitterdust last long enough to still decide the combat from the first round. And some of the key spells that were nerfed were ones that specifically helped others in the party. Grease, for example, was often used to keep foes flatfooted so that rogues could easily sneak attack them, and now that's out the window. Furthermore, as long as other books that are full of strong spells can be used there will always be a way to get "I win" spells, since those spells are untouched by any attempts at balance that Pathfinder makes. And then there are all the spells that weren't nerfed... (Hideous Laughter, Hold Person, and Entangle come to mind.)
3. It is backwards compatible only to the parts that make interclass balance worse. Backwards compatibility isn’t just a marketing buzzword used by Paizo. It’s a term that has, if not its origins, a good part of its popularity in software engineering. A newer version of software is “backwards compatible” with a previous version if you can, without any alterations at all, replace the previous version with the newer version (this is important with software, otherwise you’d have to rerelease every binary ever that used a new version of a library, which is just infeasible).
Pathfinder is very obviously not backwards compatible with 3.5 if you understand the term. Its combat system is completely different; it doesn’t interface with older combat feats at all. Power Attack is completely redone, etc. That means that fighter-types need to have things houseruled in and modified by hand in order to have the diving dumpster of options in 3.5 that they needed to keep competitive with the full-casters.
Funnily enough, the vast, VAST majority of spells are fully backwards compatible, because their wording doesn’t depend on the details of most other systems – they’re "function calls", things that operate by referring to other parts of the system without caring about the fiddly bits of how those systems work. The spellcasting system is also almost unchanged relative to 3.5.
That means that, apart from things like Divine feats needing the Cleric to take another feat (which, given that they get more, isn’t as big a deal), the spellcasters have almost all of their existing options grandfathered in, while the fighters don’t. That is the opposite of what needs to happen.
4. It invalidates pretty much every sourcebook and existing character that isn’t the Spell Compendium. Okay, yes, you had to convert adventure paths and the like going from 3.0 to 3.5. But it was still actually closer to compatible than Pathfinder is with 3.5. Basically, the only thing you can use in Pathfinder without transition is fluff not relating to the Outer Planes. Including previously made characters – you have to rework a character from level 1 to port them to the system, rather than just doing spot fixes.
Sure, there are a lot of things that don’t need changes to be usable – but you don’t know which those are until you’ve checked. So you have to check for everything, and make note of which things don’t need changes and which ones you’ve already changed.
5. Crafting requires very little expenditure of resources. By taking away the experience cost of magic items (which wasn't a very good limit in and of itself, but was a start), Pathfinder effectively doubles the effective wealth of spellcasters who pick up a crafting feat. No longer does the threat of being lower-level than the rest of the party deter caster from creating whatever items they want, as long as they have the gold to fund their enterprise. Meleers still don't get any access to things like this--the greatest smith in the world can make only mediocre weapons compared to a decent-level spellcaster who casts Greater Magic Weapon.