It should depend mostly on how you want to use it. Most jet boats around here are flat bottom and are run mostly on rivers and occasionally on the lakes. I have never seen a tunnel hull flat bottom jet around here, may be a few, but not common.
If you plan on running mostly lakes and bigger rivers a mod-v might be a better choice. With that being said I have never been in a mod-v, only flat bottoms.
When I ordered mine in '02, my main plan was for gigging. A flat bottom is more stable, runs shallower and is very suitable for jet use. 3 people can stand across the front deck and I can stand on any corner of the boat with little movement. Though my boat is also wider than most, with a 60" bottom and 85" across the beam with 28" sides. Yes they do slide in the turns which takes some getting use to and are rougher riding in heavy chop and waves. After 12 years of use, I would build it the same way today. I run rivers and creeks the most, from ankle deep water to water not much wider than the boat. I also use it on smaller lakes around here and Lake of The Ozarks several times a year (mostly at night and in the upper part of the lake).
Just my .02 worth, Good luck and enjoy whatever choice you make. If at all possible see if you can get anyone to take you for a ride, should help with your choice.
Give www.trouttandsons.com/ in St. James, Mo a call, they will be able to answer any questions you have.