Alright, I'll throw my hat in. I will also echo the subjectiveness of this; It's a highly YMMV zone, and sometimes, what some folks favor, others don't. But I'll go down the list here of some of my own personal likes and dislikes from the changes. For a bit of background, I started Shadowrun in about 1994, with Second Edition, and have played almost every character type. I'll be comparing 3 and 4.5.
Personal Pros of 3e:
*I liked the power level of starting characters. (See Con of 4e section for a better explanation.)
*I loved the pools. Combat, spell, and the like-I liked the extra layer of strategy they involved.
*I like how high skills actually strongly meant something, but at the same time you didn't want to neglect your attributes-but Skills still held a lot more weight.
*Rules were spelled out very clearly(see Cons of 3e, however.)
*Variable TN's. I loved these, and I felt they just generally made things a bit more meaty somehow.
*Magical flavor overall. I loved how mages and shamans worked, the additions that Magic in the Shadows brought, and the whole nine.
Personal Cons of 3e:
*Some of the rules, while tightly written, could be tough to find. They were well spelled out, like I said, but sometimes we could waste a lot of time trying to find a particular rule.
*Vehicle combat drove me bonkers and actually drove me off of playing riggers.
*Matrix combat drove me almost as bonkers, though it didn't quite scare me off of hackers.
*Didn't like the martial arts rules too much that came later.
*Variable TN's had a darkside-as mentioned, some things could take forever if people ended up with horribly high TN modifiers.
*Cyberlimbs were extremely, IMO, badly designed. It's a 'man meets magic and machine' but cyberlimbs were just horribly priced and underpowered for what you had to pay for them.
Personal Pros of 4e:
*In a direct opposite of a 3e Con, Cybelimbs in 4e are just *so much better* in every which way. They're actually affordable(for a game that was about crazy chrome stuff to start-you should have seen some of the old artwork-cyberlimbs were insanely expensive to tweak out and you could only really do one if you went that route.) I cannot praise what they did with cyberlimbs enough.
*Easy to teach, that's for sure. I think partially the writing and partially Skill + Attribute rolls, I find it quite easy to show new players.
*Book is generally, IMO, well laid out and stuff is easy to find. Very nice looking, as well. Has some excellent support books as well(I love Augmentation and Arsenal.)
*I much prefer 4e Martial Arts than 3e. I have a lot of fun with these.
*Vehicle rules made me want to play Riggers again.
Personal Cons of 4e:
*I may be a bit basted for this, but here goes. I preferred the general higher character power in 3e. I LIKE playing my 'higher than average' badass. I like a low to moderate power game now and again, but 3e characters seemed like they've been around the block a few times. Now, with Karmagen you can bring that back-and I'm not talking even about uberpower munchkin land. I'm no fan of a munchkin who can do it all and never fails. I personally just prefer a character who can be a little heavier out of the gate, and I find 400 BP rather restrictive in that. This also goes into my second note. You CAN make some pretty powerful builds with 400 but it requires metagaming and often stretching out your concept; that's another thing-while I like a power level a cut or two above average, I don't like to metagame heavily to get there. Now, this is fixed with a houserule-but I actually find sometimes tacking on or taking away BP can cause some pretty weird balance issues that I didn't get using the 120 Build Points or Priority of SR3.
*The BP Chargen system is just...sloppy, IMO. First off, it brings in metagaming even more than I like to. I love a good bit of number tweaking, but I don't like sinking my concept. With this, people have actually run into ''Damnit, I need 20 more BP. Well, I guess i can play an Ork!'' I just think 4.5 would be stronger overall if it just defaulted to the Karmagen system(using the German eratta-5x Attribute, racial cost.) Karmagen has it's flaws, many of which have been discussed(the two big ones are the near necessary houseruling for Awakened Human to even be able to have them get the same stat spread as 400 BP, and the fact that races with high stats need to pay a lot to actually focus on them.) It's not perfect, but I feel it just works *so* much better than the BP system.
*Not a big AR fan. Gimme an old fashioned cyberdeck. Pure flavor here.
*High Attributes hold much more weight than high skills. I also don't like the artificial skill caps.
*Magic flavor change. Mostly fluff, I did prefer the Hermetic=Elementals Shamans=Nature spirits, and then there were other versions of that. Shamans having to purchase their Mentor Spirit.
And that breaks it down for me. Even though I seem a bit hard on 4e, I still play it a lot these days-I just use Karmagen for character gen and sometimes still have cyberdecks make their appearance.