Houserule out the "Control" aspect from the spell.
The problem with the spell isn't so much that it calls in powerful monsters, in my experience. It's that it instantly gives you powerful but obedient slaves.
Calling in a Solar or similarly powerful creature isn't something I would like to cut from my D&D experience. What I would like to cut out is that any random Wizard with 9th-level spells can call in a Solar, tell it to make a sandwich, and it goes "yes master". There's no defense against this mind-control for the Solar, no saving throw, no action requirement, just control by the caster as soon as the creature is through the Gate. And that allows shenanigans, increasing the caster's ability scores being the least of which.
Now, if that control were removed, it would remain a powerful and supremely useful spell. You can still call in a Solar when your party is fighting a Balor, I'm sure the celestial would be thrilled to join the fight. You could call on it for advice. You could even ask it to increase your ability scores, which it might, could you convince it your being slightly more intelligent/strong/quick/whatever is a worthy use of its Wish ability. You just can't make it do things it ordinarily wouldn't do, by virtue of the Gate alone.
As a bonus, I'd say the spell now has far more narrative potential. "YOU DARE SUMMON ME, MORTAL?"
To answer the question rules-as-written:
Wherever the DM thinks appropriate. There appears to be no answer beyond that (especially nothing as specific as a table of default destinations) using official 3.5e materials - 3PP d20 material or earlier editions may be another matter.
For a more useful answer, we need to go beyond rules-as-written (which after all is the whole point of having a DM in the first place.) The best answer therefore depends on the style of game being played, of which there's infinite variation but here's a few ideas:
The narrative answer:
Wherever adds a good story twist, which probably means a populated area with NPCs to interact with. If it's the PCs first visit to that plane, a large city would probably be a good way to introduce them to the plane, as well as providing a useful home base. On the other hand, a small settlement would provide for more intimate interaction with local NPCs and lead to easier story hooks.
The conjectural cosmological physics answer:
The 3.5e Planar Handbook (p151) mentions planar breaches between planes, where the dividing line between two planes has worn thin. It follows that this would be a likely entry point to another plane, as the barrier between the two would provide the least resistance at these points. Planar material could be flowing in or out of this breach depending on the relative density of the planes concerned.
The Hollywood movie answer:
As mentioned in the opening question, there may well be a specific location on the destination plane that is related somehow to the point of origin of the travelers. Travelers from the plane of water may arrive in the middle of a lake or ocean, for example, while those coming from the plane of fire may arrive in a volcanic area.
To the best of my knowledge, there's no definitive list of these, and in many cases it's necessary to tweak the idea to something that would be appropriate on the destination plane - arrival from Mechanus may seem difficult to do if the destination doesn't have clockwork, but a ring of standing stones shaped like cogs feels like a good fit.
The random chance answer:
The DM grabs whatever maps or charts they have of the destination plane (sketching something out if necessary), makes up a grid reference scheme if needed, and rolls dice. Having a few easily adaptable generic maps at hand (with some locations that can easily be tailored to any plane) can be useful here. Tables would work equally well if preferred.
The murderhobo answer:
The PCs arrive at the entrance to the lair of planar monsters that need to be killed, because... they're not currently dead enough, and they have valuable stuff to take.
The "Teach them a lesson"/"My players are masochists" answer:
(Thanks to Zachiel for - unintentionally - reminding me to include this)
They arrive in the worst possible location. Covered in flames on the Plane of Fire, drowning on the Plane of Water, inside solid rock on the Plane of Earth, between two rotating cogs on Mechanus, five thousand feet above one of Arcadia's layers, etc. You'll probably never run into the problem of unspecified destinations ever again...
Best Answer
There's nothing wrong with “plot magic”, and in fact, as a 2e DM you're severely handicapped by restricting yourself from using plot magic because the system is built with the firm knowledge that DMs know they can use so-called plot magic. (The cultural revulsion against GM fiat and anything that even looks kind of like GM fiat was born during the 3e era, which is why 2e doesn't have the explicit rules about what the DM is and isn't allowed to do that people now expect as part of a D&D edition.)
To make the methods available to your players, simply move the locus of the plot magic until it's not really “plot magic” at all. Instead of plot magicking up the pocket dimension of this adversary, just fiat up the spells and rituals the adversary used to create it, put those into the world, and let them be learnable by the PCs through discovery or research just like any other custom spell or ritual. You already have the game's permission to do this kind of thing.
Balance concerns are understandable, but somewhat misplaced. Official 2e material isn't balanced in the sense that is usually meant in the post-3e community, since strong balance wasn't a design concern of the system – every home table had its own view on whether balance mattered, and something that was balanced in one group would be unbalanced in another, so no official attempt at balance-as-we-know-it was ever bothered with. By making your own custom spells, you're actually more likely to create something that is balanced for your table than if you used homebrewed spells developed by someone else for their own group.