I just finished playing both these classics, and thought their differences were interesting. There's definitely pros and cons to both games, but I thought it would be interesting to compare their biggest differences. Core combat is mostly the same, the biggest changes are the upgrade system, the collectables, and the "gimmick levels"
WEAPON UPGRADES
Going Commando:
You get a gun, it upgrades only one time, very often turning into a very different gun. The Lava Gun > Meteor Gun being the biggest change.
Up Your Arsenal:
Guns have 5 levels (ignoring NG+), and they get incremental upgrades, mostly damage increases, but sometimes mechanical changes too (lock on, secondary damage, explosions). Most guns don't significantly change until they hit level 5. I think I prefer this version, since the levels come faster, and the changes are always something you want (except for The Devastator's useless missiles upgrade)
COLLECTABLES
I think Going Commando has a much better use of collectables, turning platinum bolts into illegal mod currency, rather than buying skins that look worse than regular armor in Up Your Arsenal. At no point in UYA did I want to collect Titanium Bolts or character trophies
"GIMMICK LEVELS"
anything that isn't a run-through-to-the-end level. Both games have Arena Matches, Clank Missions, and Mining Missions. GC has Pod Racing, and Space Ship Battles. UYA has Hovership Missions, Battle Missions, and Quark Vidcomics
I think I much prefer the gimmick missions in Going Commando. There is like 3x the amount of Arena content (I love that the most), and even though the pod racing was boring, I can't believe they got rid of the Space Ship missions in UYA! Those were legitimately so fun!
UYA introduced Battle Missions, and those honestly were just like a regular planet, but broken up into pieces. I absolutely hated the Quark Vidcomics, as a one time thing, it was charming, but it's so boring to make it mandatory to do all 5.
I may be in the minority, but I liked the planet mining stuff in GC. The desert level especially. It was fun just relaxing, upgrading my weapons, and getting bolts the whole time. The sewer crystal level in UYA was annoying. It was cool you could gravity-boot up the walls, but that will get you lost quick. Just a slog to get through.
Overall, I think I prefer Going Commando over Up Your Arsenal, but they are very very close in quality. I'm starting up Deadlock, next. Hopefully that will scratch my arena itch