I just rewatched the whole first season during the last weeks and I noticed the exact same thing. I had always hoped that all the loose ends would be taken up again at the time. Then I almost forgot about them.
I couldn't believe that Jones only wanted personal revenge. I mean the ZFT thing seemed to be so important during the whole season. They were introduced as basically the main villains in the show and then Jones died and we never heard of them again... Quite underwhelming.
I also thought it would be nice to see more of the cortexiphan activation tests. They seemed fun