Yeah Mekkah, that is true. The budgets are entirely separate. They could cut all the prize support out of TCG entirely and it wouldn't change anything in VGC. As Mekkah said, the budgets remain the same, but they need to expand the player-base all the time. This means more events, which also increases the amount of players, but due to more events the prize support has to take a cut in order for prizes to be available at each tournament.
They are able to save money by having TO's host everything, but for the most part these people are volunteers. Maybe we need more people to do this and it is a big workload for them now that they have to keep up with everything in VGC as well as TCG. In an ideal world, all tournaments and leagues would have a TCG expert and a VGC expert. This could be something for each of us to put forward to your local League Runner if you want to try and boost the amount of people playing VGC. I can't see us getting much more prize support in the future, but I reckon Play! Points will come into it somehow. The more you earn, the greater prizes you can purchase with them. Think Nintendo Club points each time you buy a game.
Some TO's will obviously charge a small fee to entire tournaments. When I used to play TCG at my local League, they did £3 tournaments most weeks for fun, where basically everyone got a TCG booster for their £3 entry and then got to play in the tournament to determine who would win a couple of extra boosters. They also charged £5 to enter the more premier events, and of course even more for pre-releases.
I for one, would gladly pay £5 to enter smaller, but still premier VGC events. Ones that mirror TCG tournaments (City, State, Province) and go towards a rating. The only thing is that this would probably not go towards TPCi and their prize budgets, it would go to the TO's or the store / venue they are playing in. Unless TPCi require TO's to note down the number of players and entry fee, then allow the TO to take a percentage. I just hope we can expand VGC more in the future, like everyone wants. However, I'm happy enough with what we currently get and it's obvious they are still at least trying to expand year upon year.
We don't really have much of a right to complain about how things are going right now IMO.