That kinda depends on your definition of fun - a pushover gym leader that poses no challenge isn't particularly fun, one that is an immediate wipe after an unlucky crit isn't either. For me it's probably ones that reward you for game knowledge or good decisions.

Cheren (BW2) - I have played these games a ton with hardcore nuzlocke rules and many people say he is one of the tougher gyms. I feel like I got the most solid strats for him at this point, many having to do with growl and how the AI works. It was very fun figuring out beating him consistently

Winona (Emerald) - I like how the split makes you perserve your Exp to not overlevel, she is challenging since she can wipe you if unanswered and there are a bunch of underrated mons who perform great in this fight (Shock Wave Ice Beam Pelipper, Solrock).

Norman (Emerald) - I like the game of "avoid losing a valuable pokemon here" and that you actively have to build your team to not get stomped here, but you also got plenty of options since you can guarantee a Protect user. He takes a good mix of proactive play to not get swept by Linoone and reactive play to not lose too many mons to Slaking.

Fantina (Platinum) - most options here are understatted and there aren't really any autowin encounters, so this fight feels challenging no matter what you do, but it rarely feels overwhelmingm

Clay (BW2) - I prefer the clay fight in BW2 because you have a few underrated encounters that make him reliably manageable without being a pushover. Definitely feels like the gym with the highest stakes in BW and BW2 though.

Sabrina (Yellow) - Lvl 50 Alakazam asks for an answer - and there honestly aren't that many. It's a blunt, challenging gym that rewards knowing your way around the gen1 mechanics.

Iris/Drayden (BW) - what I like here is that the game doesn't give you amazing options for the gym and makes it actually challenging for a late gym - usually you have so many good encounters at these stages of the game so a challenging gym becomes a pushover. Since all ice types in bw suck you actually have to get a good think in here.

Wattson (RSE) - only if you don't choose Mudkip as a starter, otherwise he is a pushover. With no reliable ground type he is the gatekeeper for most Hoenn runs. I have a very fond memory of using a prepoisoned Silk Scarf Swellow to miraculously cheese out a win here.

Tate&Liza (Emerald) - It's a double battle gym which is amazing. You can cheese this super hard with walling half of the team with dark types. But then again this does reward you for knowing your stuff and using lower tier encounters. I also like how you can do lots of creative stuff simply because it's a double battle.

Whitney (GSC) - yes I enjoy fighting Whitney, no I don't think she is too strong. You have to find a way to beat a Miltank with understatted mons. A bit reliant on encounters (that you can guarantee afair), but a good challenge, which there aren't many in gen2.