All the power, skill, and weapon upgrades appear to require a second playthrough. This is not correct.
What you want to do is save up a specific amount as follows:
Weapons: $5000
Skills: 3 Points
Powers: 3 Points
Now, if you look at the trophy meter, buying a new upgrade will increase that respective achievement. If you save before doing so, and reload to buy it again, the trophy doesn't give further progression (for every other trophy in the game, it does).
However, if you buy an upgrade and reload, you can buy a different upgrade and gain progress for it as well.
So, you can get this trophy as long as you reload and buy every skill at some point. The game won't check to make sure you have them all right now. At the end of the game, I didn't have enough. I just loaded an old save where I had a lot of everything saved up, bought new stuff, reloaded, bought more, etc. until I had the trophy completed. Easy!
This should save you a huge amount of time playing through 1/3 of the game again.