I agree. I really disliked the design decision of making the game purposefully imbalanced to promote system mastery as a game factor.
This was a decision made back with the design of 3.0e, when WotC took over. I'm guessing, but I'm pretty sure, that the decision was pushed hard by WotC people who saw how much MtG was bringing in, and felt some similar design process was needed to make D&D successful.
I'm of the personal belief that the Player shouldn't have to be concerned about making poor decisions that can drastically alter his choices and "power level". If the game design is done well, then the Player can decide to choose whatever he wants, because of theme, flavour, or fluff even, and still be at least reasonably close to a power level as the "optimal" choices.
The reason having a wide variance in power level for a given level is bad is that it makes the tool (APL, Character Level, CR, Encounter Level, etc) that much more useless for the DM to adjudicate his game.
It's bad enough when the disparity is between the party and an adventure path or a PFS game.. gives the DM more work to do.
It's at it's worst when there is disparity between players, because now you have the problem where one player might not be getting as much "spotlight", which can make the game less fun overall.
I guess it can be summed up into one sentence: System mastery creates an environment where there's fairly good potential for the loss of the primary goal of playing.. fun. And DM heaaches.
Okay, that's two sentences.
If I were to make changes, I would personally like to go through a lot of the basic feats (Power Attack, Combat Expertise, etc), and make many of these simply combat options, like fighting defensively and maneuvers.
After that, I'd make feats scale more. If there's a feat that is basically replaced by a later version (or the later version just tacks on something to it), you only need the one feat. Two-weapon Fighting and Vital Strike, I'm looking at you...
Finally, I would reduce the feat "tree" requisites. Keep ability score and other requisites, however make a feat need "one of" a selection of feats as a prerequisite, or just using BAB minimums. Whirlwind Attack being the greatest offender, but it's not the only one.
Ultimately, I'd love to move D&D away from the "bonus" side of things, and focus more on lateral improvements; gaining more functionality or easing restrictions, rather than just giving an extra +.
This would take a revamp of the system though, as a lot of the "other side" (monsters, traps, APs encounters, etc) are designed around the level of bonus scaling that's currently in place.
Something for the next edition, perhaps.