Myself, I can't really find fault with this new system when I'd actually suggested something similar some years ago on here. At the time I kept thinking about how the ruleset they were working with just wasn't working anymore - Fallout 3 had some serious balance issues I felt, and New Vegas only mitigated what I feel were some pretty foundational issues with how they'd implemented the system. It was all too easy to start running out of places to dump skill points into ("well, this character has never so much as equipped a grenade or a rocket launcher but I guess I'm going to start getting 100% in Explosives just because there's nowhere else to dump them.")
And on top of that there wasn't much in the way of a unifying mechanic in how these skills were implemented into the game. Sometimes you made percentile rolls, other times you needed to reach a specific threshold. When firing a gun in real-time your stats had some nebulous effect on things but then when you used VATS that was an entirely different system that didn't relate to the other systems at all. To me, it's like if I was playing Dungeons and Dragons and if sometimes I rolled a d20 to see if I hit something, but then other times if I wanted to attack something I drew from a deck of playing cards. One way or another the whole thing needed a revision from the ground up.
I'm quite looking forward to seeing how the new perk system works out. I think leveling up and then picking one thing to advance in for that level (be it an attribute, skill, or utility perk) could be rather interesting.
More importantly, I think it might be a better fit to the game that Bethesda has been making anyway. An open world action RPG is not the same thing as a top-down turn-based RPG. I happen to think the idea that you're going to wholesale try to transplant a system designed for one playstyle into something that's functionally so very different is just silly.
One thing I'm most excited about is that it feels like it'll potentially allow for more individual and unique characters - with so many perks and levels to pick from I highly doubt I'll be maxing everything out before I finish the game, unless I specifically try to grind my levels up. Which I'd contrast with Fallout 3 where I just up and hit the level cap before I felt I was even close to finishing the Main Quest. I'm even hoping they just remove any level cap - if you want to grind all 200+ levels to get everything in the game, then by all means do so; I'd just like to not to have to worry about that happening to me unless it's a goal I set out for. It shouldn't (in my opinion) be something that's just a side effect of playing the game. I didn't even max out Batman in the Arkham games until I had completed the game and was trying to collect all the Riddler trophies...
My only real worry about the new system would be that I really liked getting those quest-specific perks or the one-off ones. Perks that you don't earn by gaining a level, but you have to complete something in the game to get it (like Excrement Excavator in the old games, or the "Kill 100 Insects" stuff from New Vegas.) I just hope that the perk list isn't all the perks we'll ever be able to get, that there's room for more "story" perks and whatnot to earn.
Of course now we've got a serious semantics issues with many of the terms in the game (Perks aren't really Perks anymore, Action Points bear no mechanic resemblance to AP from the old games, etc.) But I don't tend to worry too much about naming conventions. Technically, these are no longer Perks, by their previous definition - but that's a semantics thing that I'm not going to bother debating people about.