It's going to be pretty tough for JT to win the Heisman in a run-first offense as the QB. That's just the way it is. I'd put Conner first, then probably Dalvin, then Watson/Thomas.
I mean, look at Thomas's stats this year. They were good, but he still barely completed 50% of his passes. He passed for under 1600 yards, 17:5 TDs, and less than 1000 yards rushing (all this despite playing in 13 games). He had two games throwing for more than 150 (Wofford and UNC), and only four games rushing for more than 100 yards. Thomas is also losing most of his supporting cast, which will hurt his numbers to a degree.
To be fair, I disagree that Watson should be #1. That said, he came within about 100 yards passing of JT despite really playing in 5 games. It's a bit unfair to say that Watson had a good game against only UNC - he also threw for more than 260 against FSU (with a 68% completion percentage); against NC St (59%); and SCe (74%). He threw 4 TDs in those games with no picks. Also had the same amount of rushing TDs as JT. As a freshman too.
The guy I'd actually give the #1 nod to is Conner. Returning offensive (and overall?) player of the year. He had a single game under 40 rush yards; every other game was over 75 (including 6 over 150 and 3 over 200). How does a guy with 1675 yards and 24 TDs as a Soph not get the nod? Maybe Pitt as a team isn't good enough but that dude is completely legit.
Kaaya's numbers were solid (nearly 3000 yards passing, 58.6% completion), but the 25:11 TD:INT ratio isn't elite at all. He was also erratic, with only three games more than 300 yards and another three more than 250. If he lowered his INTs he'd be solid, but I'd still put him behind the others (esp w Miami at 6-6).
Dalvin I'd probably put #2. For starters, FSU will win enough games for him to actually be in the mix, which is less likely for the other teams. He also ran for over 900 yards and 8 TDs despite having only 3 games of more than 15 carries. He had really good games against Syracuse, Louisville, Miami, BC, Florida, and us.