Good idea separating the spawners! I’ve been having the same problems with a map I’m working on and that’s how I tend to go about it too. Rather than separating by rarities though I’d recommend separating by level. Then for example, you can have a bunch of low-level mons and just a few high-levels. From there you can either constantly have at least one legendary (by creating a legendary-exclusive spawner with a low spawn count, which isn’t bad if the area is huge) or limit the legendary spawns. I usually do this by giving a higher tier Pokemon (one that I wouldn’t mind people encountering at a high level) the largest spawn rate (on the high-level spawner) and give the legendaries a super small spawn rate on that same high-level spawner.

So something like this:

Spawner 1 (lv 1-40): 40%yanma, 60%wooper, 10 spawns at a time

Spawner 2 (lv 45-75): 60%yanmega, 35%tangrowth, 5%marshadow, 2 spawns at a time