Some PhD are using Isabelle too. I'm not so much against Coq and pro‑Isabelle, and more see good and bad points with both. As a summary : Coq has a logic where type as proof and Curry‑Howard isomorphism are immediately apparent, while Isabelle is less obvious with this; Isabelle has a nice and structured proof language (except for its keywords) and generate nice proof texts you can read outside the Isabelle environment, while Coq proof looks less natural and can't be read outside of the Coq UI and its display of proof's states; Coq makes use of clean and readable plain English keywords à la Ada, while Isabelle use confusing and abbreviated/cryptic keywords; Isabelle's favorite logic, HOL, is more famous and more well know than Coq's logic, CoC; Coq core system is simply an implementation of its core logic, while Isabelle first implement a meta‑logic in a system which is hard to understand really; Coq UI is more fluid and lightweight (native GTK) than Isabelle UI (jEdit and Java); Isabelle is implemented in SML (safe), while Coq is implemented in an alleged safe subset of OCaml (which is unsafe to me).
Both share some bad points: hard to generate program source outside of their native target (SML for Isabelle and OCaml for Coq); generated program sources make use of infinite precision numbers only (bignums are not efficient); both are better suited to purely mathematical proof than to programming, although they are both advertised as being able of this.
That's what comes to my mind trying to reply quickly.
By the way, I planned to have a look back at Coq in the future (just to say that I don't hate it).