I really don't think you can compare 1upt/city defense, that's one of the defining factors between games and each works in its own setting. 1upt is more fun to fight with but at the same time I do prefer having very large armies of 20+ where each unit only takes a handful of turns to build and isn't so important on its own. City defense is great, though.
Science is decent in V but I have to say I prefer the way it was in IV, where managing your economy is more of a balancing act than just maximizing everything. Also, tile improvements were way better IMO in IV both by being interesting and the awesome feeling of seeing 8

river towns. Also I absolutely HATE maintenance on roads, it slows your units down unnecessarily and adds a gold drain in a really unpleasant way. Those things I feel are all symptoms of having science separate from the economy, I really think the way it works in V is fine it's just everything that goes along with it isn't as good, IMO.
I do really enjoy Social Policies but I honestly don't feel at all like they fill the role of civics. I prefer having the government be a feature in the game and I loved the way civics did that. Social Policies are really fun and go extremely well with the nationalized culture, I just don't see them as being a worthy replacement.
Hands down have to say I prefer local happiness and health to collective happiness. It is a perfectly fine mechanic in V for controlling expansion but just cutting health and the realism aspect are kinda lame.
Religion was fun and just cutting a feature like that is never great but it had its issues and I can't say I miss it that much, it was as much of a hassle as it was useful and I don't think it'd add too much to V, plus the most essential bonus of giving some culture to each city is covered by SPs.
I do prefer hexes to squares, very minor feature IMO hexes are just a bit better both combat and realism wise.
The culture thing's my main issue. First of all, I absolutely love the concept of national and local culture, I think it just makes so much more sense than having each city of the same civ completely culturally independent. Having national culture add up to give benefits to the whole civ is great and really fun, I just really like how it works both ways. I feel similarly about happiness, ideally I'd like to see happiness locally managed but having the entire nation's happiness still add up in the GA meter, that's a great feature much like national culture and I just really like how it works. However I still voted for Civ IV on the culture one, for the simple reason that I HATE HATE HATE ABSOLUTELY CANNOT STAND that cities get one tile at a time, slowly slooooooowly pick up the area around them that their citizens work and then NEVER EXPAND AT ALL beyond that. Seriously, my #1 beef with Civ V, well close to how restricted expansion is but now that SP costs are more reasonable even worse than that, is the huge areas of wilderness covering so much of the map even into modern times. I absolutely hate it, it just kills the immersion for me. Having one square here and there in the desert or on an isolated peninsula is fine but every single game of CiV inevitably results in tons of empty spaces that are unclaimed by any nation because they aren't good enough to be worked by a city, and they just sit there empty forever. I hate that, I want those all in my borders dammit, just because people aren't living there and working doesn't mean my nation can't even fill in the continent it's on. Honestly the 1 tile at a time cultural expansion works pretty well, at least as well as how it was in IV, but it directly leads to the huge empty spaces issue and it's just in no way worth it at all, this outweighs for me even the much improved system of national culture, it's just so awful.
So, yeah, I'm a Civ IV guy at heart, definitely prefer it to V but it's a different game and now that V has been patched to release quality it's a great game as well, it's not the classic that Civ IV was but outside of a few issues it's worthy of the Civ franchise.