Looking to get rid of my VFR 800 and move to an FJR.  Specifically I want something that's a bit better suited to 2 up riding with my wife but I'm not ready to go full Goldwing.  Something that can still be fun and sport-ish to ride.  I realize Goldwings since the 2000's have been much sportier than you'd think they are....but still not ready to go there.  Besides, I've entertained the idea of an FJR since they were introduced.  I just like them.

That being said, is there any reason to choose a certain FJR generation over another?  Aside from "newer = better" and "older = cheaper"?  Looks like they break down by 03-06, 06-13, and 13+?

I have a 2005 FJR, fast and comfy it eats the highway miles. The closest thing to a complaint I might have is that it has no quirks. It is simply reliable and predictable. After awhile that can be boring. If you want boring, reliable, efficient and effective it is a great choice.
I don't know much about the later generations but I heard they are even better and more refined. Regardless they are great bikes.

Don't rule out the Honda ST-1300. Can be had mighty cheap for some reason.

Ride with a couple of guys who love them. Each of them are on their second FJR after having put many miles on the first. Fun bikes to ride. Comfortable. Go rent one for a weekend and test it out.

I’ve never ridden a FJR but IIRC from magazine reviews the early generations were 5spd and when they finally put a 6spd in the bike it made a good bike much better.

My last street bike was an ‘02 VFR800 - agreed it was lacking for 2 up.

2009 here, great bike that’s been to 7 states.  I’ve also done 2 up that’s been comfortable for the short trips that we have taken.

You want one with cruise control, which started in 2013.

The stock seat is terrible. It's easily the worst stock seat I have ever used. Sargent makes a fantastic seat for around $600.

The rear shock is okay for solo riding, but complete crap two up (soft spring and not enough rebound damping). Penske makes a good one for $1,200.

If you want to use a top case, you must buy one with a metal support bracket. The Yamaha mount is plastic and will break. I believe Givi makes it (the Givi SR357). Yamaha also makes a case and aluminum bracket but it's over $1,000!

The bike is heavy.

You may want bar risers if you are over 6'.  

With those few upgrades the FJR really is a great handling and fun bike. They are not super fast due to the weight but are smooth and have good torque. The electric windscreen is a cool touch as are the heated grips.

I owned a '02 VFR800 for 9 years, then a '10 FJR for 11 years, and now have a '21 Goldwing. I can tell you for an absolute fact, if having your wife along with you is important then you want the new generation Goldwing over a FJR. I really liked my FJR though, it's a great bike. But it is not that comfortable for long rides, especially two up. They definitely need a replacement seat, and mine had a Sargent which never really was that comfortable either. The FJR is a top heavy bike and a fairly heavy bike, and it shows in handling. Even though my 'Wing is a lot heavier, it feels much lighter due to the super low CG. It's a joy to ride. It'll never be as sporty, but it does the job you are describing way better than my FJR ever did. I miss my old VFR big time, but since getting the new 'Wing I don't miss the FJR at all. Not a bit. IMO the FJR is one of the great sport touring bikes, maybe even the best. It smoked the ST1300 in comfort for me and the misses by a huge margin, and is way more fun to ride. It's a great choice, but don't brush off the new Goldwing too easily, Honda trimmed it way down and gave it some much needed fun factor with the new generation (and especially with the DCT!). Worth a test ride at least if it's in your budget possibilities. You can't go wrong with either of your choices though.But seriously if you put your wife on a 'Wing, you will be told you are buying one. ;)

My buddy will ride around the outside of sport bike guys who are in his way, and he’s crossed the country on his FJR in less than 50 hours.

Fantastic bike.

Test rode a FJR before and I hated how low it was to the ground.

I love my Multistrada for the commanding visibility on the road.

The ground clearance on the FJR is not much.  Be careful going over speed bumps two up or with full cases.

STs never did anything for me.  They just always seemed soul-less.  And this from a guy who owned a Pacific Coast 800.  lol

Current gen Goldwing is out of my budget.  However the previous gen (01+) would be doable.  How does the previous gen stack up with the current gen?  

It's probably a mental hurdle...but I just feel if I'm at Goldwing point we should probably just buy a ND Miata and call it good.