We have used the kit chassis with great success for many years, but we usually modify it in some way. Here's our history:
2012--(rookie year) completely standard kit chassis, but with larger wheels
2013--Standard kit with super shifters
2014--Standard kit with sonic shifters and omni wheels on one end.
2015--Standard kit with cut out in front for tote entrance and omni wheels on one end.
2016--Fully custom laser cut chassis with actuated suspension
We will continue to evaluate the kit chassis as a viable option every season, since it has some significant advantages:
1) FREE (the first one, anyway)
2) Lots of COTS ways to modify it
3) Uses fewer engineering resources
4) Lots of support in the community
Regardless of the advantages of the kit chassis, I believe that you should encourage your team to develop alternate drive trains. Most importantly, the engineering exercise is great experience for the team members. It also gives another option to evaluate when doing your game analysis. Even if it does not get selected 9/10 seasons, that 10th season, it could be the difference between winning and losing!
The biggest advantage that I found with a custom chassis, though, was the flexibility it gave us in mounting our attachments and gearboxes. It allowed us to really design for maintenance and repair and to package things the way we wanted. This is a benefit that you'll never see from a kit chassis.