I also spent a good amount of time in academia (math & physics), wrote everything by hand (dozens of pages per day), and I, too, suffered from serious hand fatigue & RSI for years, even when using a fountain pen. My recommendations:
- Use as light and as thick a fountain pen as possible. Also, very thin & hard pen tips may be nice but in my experience they make it harder to write.
- Work on your posture (if you don't do that already). Work out your neck and your back in particular to compensate for sitting all day every day. A stiff neck (even if you don't feel that it is stiff) can seriously impact the nerves in your arms & hands and, thus, muscle tension & recovery.
My first was the Pilot Metropolitan. Still a solid pen I recommend.
My next favorite was/is a PenBBS - perhaps the 309 - I don't have it on me at the moment. I replaced the nib with a Goulet nib, and somehow made it extremely smooth. I've not been able to make any other Goulet nib that smooth - somehow got lucky.
These days I'm heavily using a Platinum Plaisir which is also surprisingly smooth (no modifications).
Every time I've paid more than $50 for a pen, it hasn't been worth it. I can't get the ink in my Opus 88 pen to flow consistently. I'm sick of it.
I'm partial to Faber Castell nibs, but the pen I bought had a grip that I didn't like, and I don't want to spend the money to try their other pens.