The first moment I cracked open my 3E book and read about feats for the first time, I knew that it was a balance problem in the making.
It's really inevitable.
But, it's not just feats. There were a lot of 3E spells that were unbalanced right out of the box such as Haste.
4E tried to fix this with spells by calling every type of attack a power, and then by making nearly all attack powers do damage plus some type of bonus effect. By doing this, they could regulate the amount of damage, how many targets the power affected, and the usefulness of an effect against other powers of the same level.
Unfortunately, just like with feats, this did not work as well as the designers envisioned. For nearly every class and nearly every level, about a third of all powers just plain suck, about a third are ok, and about a third are pretty darn good. The ratio varies somewhat, but there are very few class/levels where players say "Boy, these are all good. I cannot choose at all.".
As the game has matured, so have the players gotten more experienced. Most players now know what works well and what does not (even the designers did not really know that when they first designed 4E), so now it's no longer just feats. It's powers as well. It's not so much the feat that adds +1 damage per tier, it's the fact that the feat is doing so for the best possible power at each level.
The other side of the coin is that many players, regardless of their DM's roleplaying claims to the contrary, are playing D&D for the combat. The players might roleplay and interact, and even do so well, but they aren't just sitting at the table for the theater aspect of D&D. Very few players are really seriously roleplaying monkeys. Instead, many players are there to kill things. A major portion of the D&D enjoyment experience for many players is the combat, so players are going to put their PCs together to get an edge in combat.
You really very rarely hear about the player who min-maxed all of the roleplaying / non=combat feats and his or her PC seems worse than the rest of the PCs. There are players who often make tactical mistakes and/or designed the PC poorly with power selection, and so it seems like the PC isn't very combat capable, but it's rare that the reason is because the player took a bunch of non-combat feats.
So, one cannot really look at it in a bubble. It's not just feats. It's not just powers. It's not just magic items. And it's not just PC synergy. All 4 sides of the power gaming square add to the overall umph of the team's effectiveness.
One way the DM can fix this is by very carefully handing out magic items. Don't hand out the absolute best items, even if they are on a player's wish list. Instead, hand out items that are more situationally useful. The players control 3 of the 4 sides of the power gaming square, but the DM controls the 4th.
I don't think a DM has to put in rules on feat selection. The DM has to control the game via limiting uber magic item acquisition and by challenging the PCs in other ways such as with stronger encounters, or encounters with disadvantageous terrain. Water works great and splitting up a room with many different water ways (creeks, canals, etc.) works even better. Having monsters that come out of the water and go back in to come out in a different place works awesome. Having Artillery snipers where the PCs have problems reaching them. Having undead with phasing allows the undead to go through walls and avoid PCs. Using mazes that split the party up. Using traps that hold a few PCs in a given place while the monsters focus fire on the PCs who are not held is extremely effective.
And one of the best encounter design tools is size of room. Rooms that are large result in PCs that get split apart out of the range 5 of most leaders. It's difficult for the PCs to quickly attack artillery and controllers from 4 different directions in a large room. Rooms that are small can result in many PCs getting hit by area effects. A single narrow 5 foot wide corridor to fight in will create fits for players.
There are a lot of ways to make encounters more challenging without increasing the monster difficulty at all. The number one way to challenge players at any level in 4E is to take away the PCs advantages. For example, the main advantage that PCs have that NPCs do not have is healing. Take out the leader(s) and the rest of the PCs are in trouble. Another advantage that PCs have is Strikers. A party without strikers is a lot less effective than one with strikers. So, take out the striker(s) early and the rest of the team doesn't do enough damage to take out NPCs quickly, so the encounter becomes longer by definition, the NPCs get more attacks in, and the party uses up more resources.
Players get used to the specific advantages that their PCs have, but the DM does not have to target those specific advantages. Just by controlling the terrain and which targets the monsters attack makes a huge difference in whether the players can use the advantages that their PCs have.
Don't limit which feats the players can take, limit their magic item and tactical options. They'll hate you for it.
