Last time I shopped, in 2012, I test drove about everything I could find with a manual that I thought would be both fun and practical, mainly for long commutes. Among the midsize and larger cars, I found an Infiniti G37 sedan with a manual, which is rare but does exist, and a Hyundai Sonata, which the salesperson said was the only one he'd seen. I also found a used but modified Subaru Legacy GT.And a few first gen (before 2008 I think)Acura TSXs. I also drove a Mazda 6 with a manual and a Honda Accord Coupe V6 (couldn't find a sedan with a manual). And a BMW 328i and Audi A4, but I believe both have less room than a Jetta and don't seem to match the reliability of the others. So it can take some looking, but there are a few choices out there. You may have to travel a bit to find them, though.
If interested, I'll give a few brief takes.
Infiniti G37: Nicely appointed, lots of power, but a little numb and detached feeling. Felt more like a luxury muscle car than a sports sedan. I didn't think it was very engaging, but it was raining and the salesperson spent most of the time complaining about his job. The stick shift also vibrated a lot at speed, which bothered me.
Hyundai Sonata: Gobs of room and really nice interior. But despite having a stick it was more of a highway cruiser than anything sporty. And the one I drove was probably one of very few with a manual in existence.
Subaru Legacy GT: I really liked the car, but the one I drove had obviously been driven hard, apparantly with candy-loving children in the back. The salesperson said he used to own one and that I could expect to get 17MPG with premium. That kind of killed it.
Acura TSX (first gen): These were essentially Euro Accords with luxury appointments and quite nice. The shifter felt quite nice, too. While I liked the ones I test drove, I didn't quite love them, and they're pretty old now. Still, if you come across a well maintained one, it's worth checking out.
Mazda 6: Practical and engaging and pretty nice all around. The only reason I didn't buy one is that I preferred the Mazda 3. Also, at the time a Mazda 6 with a manual was pretty stripped (I think that's changed), but I could get a pretty loaded up 3. Which I did (and yes, I chose the 3 over signifacantly more expensive cars). Actually, give a Mazda 3 hatch a try and see if it's roomy enough. It might be.
Honda Accord Coupe V6: The one I test drove had been mistreated. Clutch was replaced at 30K miles, there were cigarette burns along the A-piller, etc. It was the only Accord with a V6 I found to try.
BMW 328i. Loved driving it, and the salesperson knew the roads to show off its handling prowess. I seriously considered buying one but decided against the financial and other baggage of BMW ownership.
Audi A4: Could only drive it at slow speeds in a busy suburb, but it felt nice inside. But after the test and sales experience I didn't give it much more thought.
EDIT: I don't know why slashes are showing up with apostrophes and some spaces vanished after a typo-edit, but I hope this makes sense anyway.