Yeah, it's a waste, in a way, but it's not your fault. It's a waste that a good female body was given to a guy. But once that is done, you can't call transitioning a waste of it. That's something you have no responsibility or power on. It's not a waste that YOU created. So yeah, it sort of sucks in a way, maybe, but don't fuss over it. The day your gender identity was formed as male (and most scientists are going to say, I believe, that it happened before your birth), the waste was decided, and certainly not by you.
So just do your business. As far as you're concerned, it's not a waste, because it's not a good thing to you. I'd compare it to "wasting" a good, awesome, expensive almond cake when you're allergic to almonds. Hell, if you eat it, you're the one who'll be wasted.
Also, as words of encouragement... While the body you have right now might maybe cause you issues with passability in the beginning, I'll guarantee you that the kind of body you have, when all is said and done, has the highest chances to make you a very attractive guy. For real. I'm not just telling you this to pat you on the shoulder. I've seen a few examples, and to be short, they're super hot.