While there was overlap the GBA was kicking all kinds of arse, though that was often more because the DS had not quite got over the touch screen gimmicks. Similarly many devs both knew the GBA and were given limited oversight so a lot of GBA versions of things were actually pretty good.
A while back I was playing the GB/GBC library and a lot of it was good simple clean fun, the GBA adding complexity on top of that often to less benefit (though other times almost perfection) and the DS going one step further.
As the DS library wore on then the limitations the GBA might have had (32 megabytes of cart, or indeed more like 16 in most, whole bunch of graphics, whole bunch of audio, resolution just that bit smaller than is ideal for many things) were not a thing and that made for some pretty nice examples of gameplay styles.
3ds by comparison pissed it all away and did nothing -- if you played the DS library you played the best of it, most decent DS devs went mobile phone... so basically 3ds has no gaems and you will have missed nothing by skipping it.
On the "I wish I was around to experience it new" then no you don't (time between releases was still a thing) but I think I would say go with DS and add some GBA from that rather than going chronologically.
Ignoring backwards compatibility, ROM hacks/freezing ROM hacks as they are today, possibly ignoring emulation (or at least giving them both GB/GBC) I am not sure which I would pick for the desert island scenario. I would be happy with either, and indeed probably happy with either in preference to a lot of home consoles (complete 360 + XBLA collection being one of the few things -- keep your NES, SNES, megadrive, PS1 and even PS2). DS might edge it out in the end but I would miss a lot of things, and several things I would like the GBA versions for but can happily deal with the DS stuff and still enjoy it.
For instance on the DS its Mr Driller is fine but GBA version, GBC version being something quite interesting, is my preference, Tetris DS is good stuff (have thousands of hours in on it as my "need something to occupy my hands") but minna no soft on the GBA is better for me (homebrew versions on both consoles also being strong contenders but the DS maybe winning there), Advance Wars on the DS does it well but ignoring the NES and GB stuff aspect of the argument the GBA stuff is pretty pure as it goes, megaman battle network 5 on the DS is a wonderful version and I can at least respect Star Force but 1-6 on the GBA is where it is at for me, GBA has a whole bunch of ports of and sequels to 16 bit era stuff, GBA RPGs do delve into the what if we don't clone final fantasy but the DS probably has the edge here both in that and wow do I love some touchscreen for managing things, GBA castlevanias might well beat out the DS stuff for me (there is a hack to get rid of the purple outline now), GBA probably has the better platformers but I could see a debate, puzzle games I would be delighted to see 20% of the quality on any modern device but the DS might just clinch it (puzzle hex being a massive part of that, or at least it doing both touch screen and buttons approaches).
