I think you just get used to what you have and it throws you for a tailspin to have to adjust.
We got the 8 passenger Sienna when I was pregnant with my twins specifically because I wanted all 3 in one row. I figured if we had 2 captains chairs and someone had to sit in the back, the kids would fight over who got the comfortable seat and who got shafted in the back. So this way they were all equally un/comfortable! My oldest was still in a car seat at the time so we put 3 across the middle and it was fine. Never even thought about armrests since, coming from a sedan, it wasn't something we were giving up. I never felt weird having a van with all the kids i the middle row since then I had the whole back for diaper changes, double stroller, costco run, whatever. It worked out great for us. The seats in the old Sienna tumbled forward rather than slide which is super easy and put the seat out of the way without removing it, so once we had kid #4 we could easily throw open the space to the back (passenger outboard), have 2 in the middle, 2 in the back. Worked great. But we had a leak in that van that drove me batty for 2 years and we finally gave up and moved on.
I had ruled out the Ody when we bought the old Sienna because the 8th seat for the Ody was lousy compared to the Sienna. The new Ody was close-ish to the old Sienna and I jumped on that fact, without noticing small things that drove me nuts once I got home. Such as what is up with the 3rd row windows not opening??? I didn't check that at the dealer because why wouldn't they??? I thought every van did. I didn't realize the seats slid vs tumbled - I assumed all seats tumbled! I was positively batty with how much I hated this car. I just couldn't do with it what I did with the old one. I hated to actually REMOVE an outboard seat because then why bother having bought an 8 person van??? If I left it in though I didn't have a spot for diaper changes and I can't trust my girls to put the seat back when they climb back there and if they don't do it right it slides around when I drive. I finally gave in and removed it. And it works. I can't fit 8 but if I need to fit another person in without warning I can move one of the girls' seats from the 3rd row to where my son normally sits and then fit 2 un-car-seated passengers in the 3rd row along with a car seat. Tight, but works. With the old Sienna I couldn't easily fit a person between the girls' 2 frontiers so I really have about the same amount of people space as I did then, if I didn't move a seat. It's not the same but I have figured out how to make it work.
We didn't even consider used with our new car because I was afraid of getting another problem vehicle with no warranty (I didn't know you can get extended warranties and so forth on used cars). Had I known you can put the captain's chairs side by side in the old Ody and take the 8th seat out - it would have been something to consider. I didn't know you could do this, though. I wouldn't have the awesome tethers in the 3rd row that the new has though... so...
Anyway. We have a Britax marathon in the middle. I think my oldest kind of uses it as his armrest. I had considered a radian because they have more legroom but I don't want to have to use a seat belt to install and it seems that works best to rf the radian? So we're sticking with the marathon until it expires. Maybe a different car seat in the middle would solve your problems?
How old is the child in the back? Can you leave the middle seat in so there is an armrest but have whoever sits in the back just move the seat each time? (Or if that seat is on the driver's side maybe move it yourself?)
Two kids in car seats in the middle, and put the oldest back in a booster in the back if he needs it?
I've pretty much worked around the differences for us. I even went and drove an old Sienna 8 passenger which still had original warranty left on it and we could have extended that even more - but couldn't commit to it. I've come to really like certain things about the Ody. I still have a soft spot for the old Sienna but have come to see the new ody not as better or worse, just different. I think that over the long haul it will be a better choice for us as the kids get older - the 3rd row is REALLY comfy for an adult so no one will be smashed back there. I don't know how it compares to the old ody though. We're done with 4 and I think this car seats 4 kids perfectly and allows a few more to be squeezed in if needed.
It's been kind of like moving to a new house and suddenly the waffle iron and crock pot can't fit in the same cabinet, you freak out, then you arrange to suit and get used to it and forget how it ever was in your old house.
I know too well that feeling of "Oh crap why did I buy this car" - and the old ones are really holding their value so it seems crazy to trade in the new for an old one. Siennas are more reasonable in price but hard to find 8 seats and I don't know what features you like in your car - the 8 seaters are VERY basic.
I hope you come around to like the new car. But taking out the putting two seats together was a silly thing to remove. The middle seat should either be bigger or you should be able to move the outer seat in - even without armrests enough room for your butt is a nice thing!
Write to Honda and tell them.
If enough people point out that they miss this feature maybe they will bring it back.
American Honda Motor Co., Inc.
Honda Automobile Customer Service
1919 Torrance Boulevard
Mail Stop: 500 - 2N - 7A
Torrance, CA 90501-2746 
