Manannan: I agree, remixing victory conditions is fine by me. I just imagine this would be part of a radical overhaul of the affinities. (Although science should gate these to a degree anyway.)
Making users unable to purchase a building may seem inelegant, but in fact it's a completely underused method of delaying the creation of an element in gameplay terms.
Design doesn't have to aim for maximum clarity; that's a design goal, not the design goal. Nor does this argument work when you're not complaining about Mind Stems (or w/e their name is) which are non-Wonder buildings that are also no longer purchasable.
Adding a prerequisite for the Trade Depot doesn't fix the problem of buying the building - all it does it increase the Energy needed to buy both at once. Presumably, that is the key issue here. Especially since Trade Depots provide Production, making it a very cheap instant boost to Production for a small city (I'd know, it was my go-to buying choice for any new city due to the incredibly low cost and the decent Production bonus it provides). Furthermore, the relevant Quest can also increase Energy or Production output further.
Firaxis' fix may seem inelegant to you, but you've just demonstrated with your suggestion that you don't even understand the core problem behind the building in the first place.
Gorb: Tsk, everyone here knows the issues with 1.0 trade routes. The thing is, they should be fixable without a "hack," so why not fix it using existing systems? Adding a prerequisite building slows things down slightly by making you buy 2 buildings outright, if you really want to punish the early trade depot. And of course it's a fix - it makes the instant purchase weaker. (Add in even harsher nerf bats if you like, such as amping up the production cost or making stockpiling energy harder. Clearly there comes a point where depots are as weak as when no purchase is allowed.)
Moreover, I think you really underestimate the benefits of clarity & consistency. Basically, a game should pick one: either a game element always works the same, or it works differently and the player knows to pay attention to it. Having one-off exceptions can be interesting if sold for *flavor* reasons, but not normally for balance reasons. For example: all Wonders can only be built once in the world. Later Civs added: all National Wonders can be built once per civ. If one Wonder was considered unbalanced, then saying "okay actually 2 can be built" is probably not the right answer, barring an excellent flavor excuse; either nerf the Wonder so getting it isn't so crucial, or make it a National Wonder so that everyone can get one. Or, more radically, make a game where the entire Wonder concept is different, so everyone expects that !Wonders all have a "total limit" that varies from 1-(num players), and they know to check that limit. So.... if you think buying restrictions are interesting, great, but make it a whole system then, don't have a totally random exception. Make it so buildings are all classed as cheap-to-buy, expensive-to-buy, and unbuyable, and it's a setting you're expected to know. That'd be fine, but it isn't what the BE patch did.
As a side note, have you ever played games - especially board games, where the players have to adjudicate the rules themselves - that are filled with tons of footnoty nitpicks and exceptions? It's potentially quite annoying, and greatly slows down the rate a new player can pick up a game and understand it. I'm a huge fan of the game Twilight Struggle, but it's one of the worst offenders of this. (Performing a coup gets you military ops. Unless the coup is via the card Junta or Tear Down This Wall, then you don't get mil ops, because that'd be too good or something, but you get the military ops just fine from the card Che. Why does Che give mil ops for his coups but Junta not give mil ops for its coups? Because the rules said so, there's no coherent design reason behind it. Or for another example, if the US controls Israel, they get a bonus in the Arab-Israeli War event, but the US controlling South Korea gives no bonus in Korean War event. Why? Because the card says so. There is no intuition about what 'should' happen in many situations, you just have to look up what the rules say.) Making Trade Depots unbuyable breaks the current BE assumption that "all buildings are buyable". Either go big and build a mechanic around this, or keep it simple & not cared about.