On the Strength Paladin vs. Charisma Paladin point:
While there were obvious problems in the original set-up (a strong paladin was forced to take a charisma based attack at level 9), the issue of divine challenge being less effective than a charisma based paladin was sort of a trade off, as the charisma based paladin lacked a good basic melee attack for charging and, more importantly for defenders, opportunity attacks. There is also the issue of Wisdom being the paladin's secondary stat. Charisma and Wisdom creates the problem of applying to the same NADs, while Strength and Wisdom applies to two different ones. The 'tax feat' that lets a Straladin make effective use of Divine Challenge (unless they have 8-11 charisma, better use than a chaladin) is balanced on the other side by a 'tax feat' for the Chaladin to be able to use charisma for melee basic attacks.
The expertise feats are probably the most egregious issue, since it applies to all characters and it has the addtional problems of forcing a choice of a single weapon (group)/implement/etc ... and further punishing people with multiple weapon/implements (who already have to pay more to maintain a magic weapon AND an implement, for example).
The defense feats aren't as much of a must have as the expertise feats. There are masterwork armor and magic items that provide item bonuses to defenses. Similarly, there are enough different kinds of defense boosting feats that, even as a "tax", you still have the option of which to take, and when you factor in the armor/shield specialization feats there is also AC boosting in the equation. While the 'hole' in the attack progression is only patched by expertise ... raising defenses is part of a combination of which stats you raise, what type of masterwork armor you use, what magic items you use, and what feats you take. Feats that can give you situational bonuses (back to the wall), big bonuses to a single defense (the +2s at paragon, +4s at epic), the ones with a secondary bonus (shield spec, the +2s at epic), or just ones that give an overall boost (+1 to all at paragon, +2 to all at epic). The only 'must have' is the Robust Defenses (since it stacks with the rest) but even then, many players would rather take an additional offensive option than boost their defenses ... and similarly their lowest defense may just be neglected as it would require a lot of feats/items/etc just to get it from bad to 'ok'.
On top of all of that, there are more feat slots to fill over the course of the character and, outside of paragon multiclassing, no huge feat trees to eat up lots of feats. The feat cost for paragon multiclassing though is definitely something that is a problem (although the hybrid model seems to be at least a viable alterative, and the 'dabling' model isn't too bad).