Cole had never had a FIP under 3.33 until last year (4.08), which was driven by an HR rate that was more that double his career high and likely a fluke. He'd fit in nicely anywhere,
But as a #3 or a #4 on top staffs with two years of control left, he's very similar to Sonny Gray. Both fit in any rotation, as you say, but how many top prospects is two years of control worth?
Also I'm not sure the HRs are necessarily a fluke, his FB seems to be pretty straight and HRs were up in general last year and maybe he is a bad fit for the launch angle revolution. Also PIT is one of the tougher HR parks and NY is one of the easier ones (plus the NL to AL move usually adds around a quarter of a run per game), so the three top prospects that it was rumored he'd cost (Frazier, Adams, Andujar in NY's case although honestly I doubt Cashman actually offered that much) is a lot.
Sonny Gray is very comparable to Cole as I said above, very similar career numbers and both with two years of control left (Gray actually 2 1/2 then), and he cost three top prospects but two were badly injured at the time, the above package is definitely a stronger one IMO. I think NY is/was better off holding out for Fulmer or Archer mid-summer once they've shown again that they're worthy of that kind of package (Fulmer had arm surgery late last year and Archer was inexplicably awful in September including leaving at least one game with the dreaded 'forearm strain').
(Sorry, I have read approximately two billion words on Cole in the last month or so since the Cole-to-NY rumors started)