Well, I'm maybe unique in that I've owned BOTH. A 2002 356 and then a 2006 36 (with a boat in between). First of all, when my wife and I decided to get a bigger keel boat again, we weren't limiting ourselves to Hunter or anything and started our search from scratch again and determined even though it had been seven years since I had bought the 2002 356, we STILL liked the Hunter 356/36 for our needs better than any other boat out there in that price/value range. So the FIRST thing I did was try to hunt down my old 2002 356 to see if it might be for sale (the answer was no). We ended up finding a great 2006 used 36 with only 25 hours on the engine. So.........
Pros on the 356:
1. Far better galley layout as has already been mentioned. The better location of the drawer unit and trash can (the trash can location on the 36 is a real pain) as well as the refrigerator preferences loom large (although I find the 36's upright frig more energy efficient than the 356's chest frig locker). We also NEVER use the separate freezer underneath the nav statioN on the 36 unless we are going on a long cruise somewhere......I like the 356's storage area under the nav station far better. I also am not enamored with the 36's "Dishes Display Area"....when seas get rough, I'm not sure those cups and plates won't launch themselves through the faux glass cabinet door.
2. The teak side cabinets in the salon are taller than on the 36 ...so more storage inside (although that means the 36 therefore has more shelf space ABOVE those cabinets....your choice, but I prefer more enclosed space)
3. I also liked the little storage area under the salon table of the 356......handy.
4. Topsides I see no advantages to the 356 except that the swim platform lockers are 'safer' in that they hinge port to starboard (as opposed to the 36 which hinge forward/aft which could be kind of dangerous in bad conditions if one of the happened to open and the whole stern storage area under the swim platform would inhale huge amounts of water.
Pros on the 36
1. The ceiling liner in the aft cabin is 'soft' vs hard plastic which saves a lot of weight and makes for easier access should you need it (just be careful wearing your Leatherman to bed ;-)
2. The removable sink faucet/sprayer combination is nice.
3. The jib winches in the back are nice but don't make that much difference when I'm singlehanding because the autopilot tacks for me anyway and it's not a big deal to step in front of the wheel to handle the jib sheets. And when my wife and I sail, we actually get in each other's way a bit more with the jib winches in the back than we would if she could just stand by the companionway to operate the winches etc. Although, if we ever do get a spinnaker, it will be nice to have the winches back there.
4. It's nice not having the 'struts' that reinforced the mast on the 356. They got in the way a lot.
5. The engine access (and steps) are a nicer set up and design
6. I might be mistaken, but I think the Yanmar on the 36 is a 29 HP vs 27HP on the 356.
7. The detachable stainless steel arch on the 36 is much easier to deal with than the one piece arch on the 356 should you ever have to remove it for repairs (not often very likely....but I remember what a pain in the ass it was to install the arch with our dealer on the 356).
8. I read somewhere that later 36's have a slightly longer water line and a more plumb bow
Beyond that, the aft cabin, heads, V-berth etc are indistinguishable between the two boats. One thing I WOULD watch for if you're looking for a 36 is that starting in around 2007 or 2008 they quit using the teak veneer down below and replaced it with a shiny cherry veneer, which was not as warm and classy we thought. Also about that time, they quit using a lead keel and went to a cast iron keel.........we far prefer the lead keel. In fact, there was a 2008 Hunter for sale when we were looking for ours and we passed on it for those very reasons even though it had some great other options.
In the end, I love both boats and the differences are just not deal killers either way. There's not a day I wake up on the 36 and say "Gee, I wish I had my old 356". Both are great boats and I can't wait to see the new e36 in Annapolis this coming week........although, I'm guessing that with all the cost cutting going on, all of us with our old 'teaky' Hunter 356/36's are going to be very glad we have what we have.