Good job finding some females in the audience (sunbathing, even) 2_Fast_4-U!
I am going to try to focus mostly on Gran Turismo 5 vs. GT3 and 4.
1). In GT4 we could install just about any wheel on any car,. I loved putting cheap black steel rims on some sleeper, instead of something flashy from BBS or Yokohama. Then after I destroy the competition they never saw me coming.
2). I miss GT3's replay system, which had a feature that randomly focused on different cars. I think GT4 had something like this too.
3). Greater selection with racing tires (super hard, hard, medium, soft, and super soft) though GT5 does a better job with tires lasting longer during enduros, in my opinion.
4). Competing against cars in real-time during rallies (not just time-trialing them).
5). All tracks mentioned in the OP, El Capitan is tops on my list. Love that scenery.
6).
7). Missions! 👍 That feeling of finally beating Mission 34 has rarely been equaled during other videogame experiences, right? Mission 34 is in my Top Ten Videogame Moments.
8). More overall challenge during slower (Beginner and Amateur) races.
9). Nitrous (rarely used this feature, but it was nice to have just in case, especially after some doofus wrecked my racing line while punting me).
10). Um... I can't think of any at the moment. Wait, yes I can. Additional tuning options, such as Stage 4 and 5 turbos. Stage 5 was better for off-road stuff sometimes. And also Org suspensions. Again, these were better for rallies sometimes. More suspension travel.
11). B-spec has more options, including the ability to
fast-forward. And also, B-spec drivers actually benefited from practicing around an empty track, meaning they could enter races already with some skill.
12). A bunch of race series are missing in the latter game. An example: NA (naturally-aspirated) races. In GT4 we get NA and turbo races. In GT5 this got scaled down to turbo races, and then only TWO tracks. I miss some of the Manufacturer's races too. In general there is less overall to do in GT5, though some may argue that a lot of GT3 & 4's races were redundant.
Here are some things I DON'T miss...
1). Getting punted by AI.
ARRGH!!!! 
2). Being forced to take unnatural cornering lines into turns so I don't get punted by AI.
3). 6 cars per race.
4). Extreme tire wear during endurance races.
5). Jeez, how can I forget?
UNDERSTEER!!!!!!!!!
6).Lack of oversteer traits, especially for most rear and all-wheel drives.
Everything from simply lifting off the gas to tighten that line, to throttle-driven dR!ft1ng, all of this is usually missing from GT3 and 4.
7). Front-end snap-back. For those who don't know what this is, try drifting just about any rear-drive (especially RDs which should be able to drift). Try to countersteer. Now try to figure out what the heck the front-end just did, as you crawl out of the nearest sand trap.
8). Lame menu music. My opinion of course, but the music in GT4 never got me pumped to race, like it should. GT5's isn't much better (opinion) but at least we could substitute our own.
9). Destroying PS2 controllers. Maybe I'm the only one here, but I used to regularly trash controllers after getting mad at the game, like Pete Townsend smashing up a Les Paul. Good thing controllers were so cheap back then....
10). Memory cards! ... and general lack of memory to save replays.
