If you're going to recreate elements specifically, then sure, you could say it might be difficult, but there is no requirement for doing so. Obviously this isn't the first time an idea like this has come up--but that doesn't mean you couldn't start working on the project anyways. You're talking about "recreating." So do so. You're not obliged to port anything. If anything, how boring would it be if you played the same exact game and system on the GBA--at least make a difference in the experience. Otherwise, we could all just play the original.
You shouldn't do something for other people. You should do something like this because you want to do it.
They don't have to be Lords. You can just assign a should-not-die flag to your leading unit of choice, which will stream a game-over should they... you know, die. ROMhacking is not about complicating things, but about manipulating aspects into new experiences.
EDIT: If you're hell-bent on retaining the ledge bonuses, you could also opt for a custom tile which will give a bonus, but that would allow every character to have that bonus,regardless of their position of height or not (at the same level or at a different level). Now, you could always justify this as being near a ledge will always give you an advantage, both because of the height, but also because you can leap down and avoid a blow.
Serious positive input! Ok then, ideas.
Defend the line; could I just set multiple tiles with an alternative nonbonus throne status, and just pile then into an area, noting them as many many thrones to "protect"?
How would tiles with bonuses be applied to only one direction, to simulate height, but not other directions? I have a vague idea, but I'm not experienced enough to say for sure.
Key survival flags, I actually thought that's what they were. Assigned to lords constantly, and others periodically (like say, Sothe). I never associated them with forced deployment, but I think they would work as both forced deployment and do not die statuses.
Also, base meetings. I already have a plan for that. Separate Gaiden chapters with a quick sieze point at a "base camp map", where only ike can be deployed, and he can visit villages to engage in prebattle conversations, then sieze the map to enter the main prep screen.