Don't know if this was discussed...
The landers - by which technology were they produced? If it's a Precursor technology, then how several of them ended up at the Starbase (if you lose a lander during the radioactives quest, Hayes gives you another one). And if the vehicle is of a human origin - where did they get it from on Vela?
The simple answer may be "Earthling Cruisers are equipped with landers", but such thing isn't said anywhere

Another possibility of "getting stuck" feature is losing a month's worth of time and appearing from a random portal after that.

Make something like "VUX start" for an Umgah? That's an interesting idea.

And an Umgah! Har! Har! Har!

Replace the Sa-Matra with an Umgah Drone! Har! Har! Har! And the real Sa-Matra would be in Umgah space, stolen long ago by the evil blobbies And you'd have to act quick to prevent THE UMGAH DEATH MARCH!!!

If one is foolish enough to go to Falayalaralfali with an Orz ship, deprive him/her of Portal Spawner (don't give quest if he/she doesn't have it yet and take it away if he/she already has it). Totally. And going to Orz space with an Arilou ship means that you'd have to fight hard to get the Taalo Shield.
Make Beta Corvi swarmed with Slylandro Probes - they are programmed to return home after 10 replications, after all
If one possesses a Druuge ship and encounters the Melnorme, they'd refuse to trade.
If disabling the Melnorme summoning feature of the 'Casters feels too harsh, make the feature cost fuel.
Delay the Shofixti reproduction time.
Make the Pkunk survive their merging with Yehat only if they reach the Yehat space after triggering the revolution.
Increase the Sa-Matra guarding force to 6 Kzer-Za and 6 Kohr-Ah.

The full classification of planets is given in Ultronomicon.

I've got a similar starmap - it came with my Star Control 3 package that also included a CD with SC1 and SC2.

And think what might come out if you add your combat system into this adventure It'll be as replayable as the original game

The beginning of the adventure would be like,
"(1)You enter the Solar system, the cradle of Humanity. You've never been here before, and you feel a bit nervous. What's Earth like? What happened to her during all those years? Were the dreaded Ur-Quan that you've heard so much about defeated? No-one aboard knows the answers...
You decide to:
- Head straight to Earth (go to page xx)
- Explore other planets a bit before going to Earth (go to page yy)
- Leave the system - you feel that you forgot something important in Hyperspace (goto page zz)"?

More with "the Playful" Talking Pet: maybe, with Talking Pet aboard, have a 5% chance of either one of your ships joining the enemy battlegroup or an enemy ship joining yours? I think it would be fun having a Chmmr attacking you and defending against it with a Kohr-Ah obtained earlier
Also... with the Utwig Bomb aboard, have a 5% chance that any hit sustained by the Vindicator during combat triggers the Bomb, thus becoming fatal.
Add some weird jokes with the useless Druuge artifacts, like: after obtaining Glowing Rod, ANY enemy battlegroups met randomly in space (except for Slylandro) have 12 ships in them. Like a "cursed artifact" in RPGs And Wimbli's Trident kills off your planet scanners, only increasing the fun
Increase the number of Thraddash ships to be destroyed to establish Culture 20.
Make Portal Spawner work only in certain days of the month (say, 1st to 4th, 9th to 12th, 17th to 20th and 25th to 28th). Also would make life harder.
Hierarchy raids on the Starbase would also be fun - maybe, have VUX/Yehat/Ilwrath (if not gone attacking the Thraddash) randomly mixed groups (the Kzer-Za raid wouldn't be fun because they'd just quickly destroy the base, effectively ending the game). The Vindicator gets a distress call from a drone (which moves faster than the flagship on full thrusters) and must react in X days, otherwise the base is destroyed and game over. Maybe, those raids would start after the player gets the Portal Spawner.
Hm, I surely got some Umgah blood in me, HAR! HAR! HAR!

Or do a search for "Vela" on the map screen.

Just off the top of my beak
Increase the price of Melnorme's technological upgrades.
Make "Evil Ones" on Spathiwa really evil and mean (to a certain degree).
Cancel the feature of using 'Caster to summon Melnorme in Hyperspace.
Increase the Portal Spawner and emergency escape unit's fuel usage.
Increase the number of Mycon ships guarding the Sun Device.
Have Zelnick actually FIGHT admiral ZEX on his upgraded VUX ship (increased thrust and turn rate, maybe) and a small fleet of VUX after delivering the VUX beast.
Have a small (5% or so) chance that any ship in your battlegroup would be acting weird (badly responding to controls, firing randomly etc.) after you get Talking Pet aboard the flagship. Before such "weird" battle, get the Talking Pet on the screen saying "The Umgah restored my intelligence, but they'd also tweaked something in my mind, and I'd become playful and humourous. I decided to have fun with some of your ships. HAR! HAR! HAR!" or something.

The first situation (with the Druuge) may be resolved with having the Druuge captain flying solo so that he hasn't any crew to burn

This whole battle system may also perfectly fit into an RPG, and there are all those Captain/Crew quirks that Clay mentioned before...

About Utwig shielding... Once an Utwig turns on its shields, he/she doesn't avoid the shots, but DESIRES to be hit and recharge the batteries. So I thought up this (if I'm getting the game mechanics correct):
Shields are turned on in the Reflex phase and last for the whole turn. A Piloting roll is used to determine whether the Utwig pilot manages to be hit by projectiles (success - the ship is hit and the shields are recharged, failure - the ship is missed and one turn's worth of battery capacity is lost).