Woow,this question is a broad question. For me being the FIFA president, the things I would've put in place for the smaller teams to also win major trophies would've been very simple.
1.I will make sure that,a bigger club will not sign a player from the smaller club if the smaller club does not want to sell.

1. Organized a short time tournament for smaller clubs to partake in with a huge sum of price,eg huge money and a bragging rights.
2. I will make sure that,a bigger club not sell a player to the smaller clubs with huge price tag.
3. I will make sure that, I tax the both clubs according to their worth. The smaller you worth,the smaller your tax.
4. Limiting a number of players the big clubs should sign and register.
5. I will try and get sponsorship deals for the smaller clubs.
6. Lastly, I will make sure I build big stadiums for them to use,in order for them to get funs.