You still wasted points with the old system no matter how you look at it. If I'm a pve player with no intention on doing any pvp out of something like Black Prince quests (which was for only one quest in the line), Why waste a point on a skill/talent that's terrible for both pvp & pve because it lead to a skill I need for pve, whereas I have more utilities with the new system (again, the new system needs a lot of work)!? It's stupid when the minor choices don't help you (the new system is guilty of this too). The trap proc/rooting proc when trapped were garbage for Hunters because they never worked when needed (not the one that triggered black arrow. I'm talking way back with pre-Wrath), and made me wish I could use the points on better stuff.
I agree you should have more options, but for the love of god, make those options worth a damn if I need to spend 3 points on a skill just to get my bread and butter talents/skill. To jump out of Wow, Look at Arcanum: over 100 stats/abilities to chose from, but only 3 of them would help you beat the game (87 of those skills were broken due to Troika's half-baked programming, and 10 were too useless like beauty). Let's also look at Diablo 2: It's stupid to waste a point on the Werewolf form if I'm going to be a Werebear.