Interesting question, and one I struggled with earlier this year when contemplating an upgrade. I agree with Coderguy - very close call and unit to unit variation probably plays more into it than anything else. The RS45 had some upgrades over the 25/35 other than 3D, but depending on how good of a unit you get, overall performance could go either way.
The RS45 is capable of higher light output and has lens memory - so if you have a big screen, or want to do 1:235 without an anamorphic lens, those are two votes for an RS45 and are upgrades independent of 3D capability. If you're a sports fan, I believe that FI on the 45 is better than what the 25 offers. At the same time, unit to unit variation means that contrast ratio, convergence and uniformity are all wild cards - and a RS25 or 35 that excels at this group of variables, could outperform an RS45 with less than steller marks in these categories.
As has been stated above, calibration wise, the RS25's built in package is superior to what's in the RS45 - you'd need an external CMS like a Lumagen, DVDO or VideoEQ to get you what the RS25 has built in.
Personally, I have a thoroughbred RS-25 (it didn't start that way - ended up like that after JVC replaced the optical block which I can only imagine was a RS35 optical block), and the upgrades for the RS45 didn't have a ton of relevance for me (little interest in 3D; modest screen size with lumens to spare so brightness not a problem; no real use for lens memories as I have a 16:9 screen; not a huge sports fan so improvements in motion/FI not a huge deal) so I opted to hold onto my RS25 for another season, versus grabbing an RS45 that might end up as a downgrade if I got a mediocre unit.
So if you have the chance to grab an RS35, or can take a look to verify that its a really good RS25, and/or value the calibration controls - and the handful of upgrades (3D, brightness, FI, lens memories) aren't critical for you - you may come out ahead that route vs rolling the dice on a RS45.