That sounds awesome, and I like it. The concept of needing to pick one Pokemon to obtain over another is not new, and we see it all of the time in starter Pokemon and fossil Pokemon, even sometimes in gift Pokemon. This would be a really cool and unique way of forcing that choice but still at least getting to add both Pokemon to the "seen" portions of your Pokedex. I approve!
Why? It's really effectively no different from having to pick which starter you want or having to pick which fossil you want or having to pick which Eeveelution you'll get in 1st gen or having to pick which Hitmon you'll get in 1st gen or having to pick which Moon Stone evolutions you'll get in 1st gen. The difference is here you still get to at least see both of them in battle and get XP for it.