I'll give you my perspective since I just purchased a JK. I started out looking for a TJ since I like the aesthetic and they are relatively simple to work on if/when something goes wrong.
Two things swayed me from that path: 1) asking price for a clean, somewhat un-modded vehicle and 2) ergonomics (mainly entry/exit for my wife with the higher door sill).
I drove a JK and really liked it and that sold it for me as far as what model to start looking for. I did go through the thought process of getting into a JL instead but around me the price is still alot higher for equivalent content. There are also more electronics so, much like any other vehicle on the road, they are getting more and more difficult to service as the generations advance. For me the styling is about equivalent - there wasn't a huge advantage there. For my usage the improved algorithms (traction control, etc) also won't be of much benefit.
In the end the JK won out for me from a "value" perspective. To answer your question specifically, what I would mainly miss from my JK is money (~$10k or so)... This is a third vehicle so not a daily driver, however, and I wanted some extra money in the budget to make some modifications.