The biggest issues I've come across are:
1) small sample size, football teams only play 16 games which means you really don't have alot of data to use.
2) counter party risk, lots of fantasy betting sites spring up and then fold, just like bitcoin. Ideally there would be a new form of prediction market that hosts bets but has a reliable third party escrow the funds.
3) Not enough volume, this is getting better but only due to Draft Kings huge advertising push this past year.
4) Lack of apis, most of these sites seem to want to cater to people who make 1 or two bets. Ideally I'd be able to make 1000's of bets each week.
If anyone else out there is working on models for fantasy sports betting please feel free to drop me a line if you'd like to discuss techniques for modelling( I believe the cool kids now call this machine learning).