I ride 99% of the time two up on my F3S.

Mostly one day rides (100mi to 300mi) and one or two long touring trips (+1300mi), and the F3S is just perfect for me.

I'll drive it almost all year as cruiser and put the cases only for a longer ride or for touring.

Have SHAD side cases and SHAD topcase, that gives me a 34.3 gals of volume cargo (vs 36.5 gals for the F3LTD).
Good thing is that I can carry two helmets just on the side cases (which btw you can't on the F3T/F3LTD, you'll need the topcase), so I can leave the topcase at home if I won't need the extra storage.

You'll have definitely to upgrade the rear shock, stock one is really weak and will bounce and bottom when fully loaded.
The two-up shock is OK, but if you can get a after-market one which is adjustable that would be the best setup.
Mine is, and I just add 10 clicks on mine when riding two-up.

Have the passenger backrest for the wife, which is great as I can remove it just with a push for my few solo rides.
Also have the blue ridge windscreen which you might want to add to the list if your considering touring.

About comfort, no complains from me or the wife. It's been good enough for long tours in Europe.

So if you're not after the audio system or the fancy dashboard, converting the base F3 does make sense.

That said accessories for Spyder are not cheap, but you might reduce the cost of the list if you can get from other fellows who are selling at a good price.