Preferring veterans over prospects in roster construction, not giving up proper chances for prospects to prove themselves (/setting them up to fail in roles that they aren't suited for), over-cooking prospects in the AHL (largely tied to the first point, and likely relevant regarding McG), coaches deploying systems that complicate promoting new talent into meaningful roles. Examples of these have been posted numerous times by numerous posters.
If I was McGroarty, it wouldn't be the first two points I was worried about - the Jets have generally been alright with top prospects, although most of them were promoted into an AHL level roster a long time ago. But as for the latter two, I'd absolutely want a guarantee that I didn't have to spend 2+ seasons in the AHL earning nothing, with the potential of only getting a fourth line job with no prospects of becoming a top six guy down the line (because there wasn't a top six spot open and nothing was done about it).
This whole issue could be down to numerous factors, but as not all of them are in the Jets' hands, I think it's best to focus on those that are - treating prospects well, making roster decisions that support their careers, and so on.