You might want to look at your mob spawning system, as even with reduced weights, less than 100% chance spawning and reduced limits per chunk, your mobs would soon fill the mob cap limit. Especially hostile mobs that don't despawn at day.
Had to keep using Opis to kill Raptors and Jabberwocks, so server players could get zombies and skeletons.
Overworld dungeons would always have a high chance of being Nether based mobs, and since the mobs are a lot tougher, they spawn faster then you can deal with (especially on Hard difficulty). Some sort of spawn control would be useful in the config.
I mostly use the vanilla spawning system (only Cinders and Lobbers use my own fire/lava based system, also Demon Mobs when spawning from Nether Portal blocks). You can individually change the spawn weight, etc for each mob via the config and all that does it pass on the values to the vanilla system, the spawn area limit should force mobs to not spawn near each other, but this depends on which version is included in monster.
Setting the global spawn weight scale to something like 0.25 should give vanilla mobs a much higher priority for both natural spawning and for any newly generated dungeon spawners. Also each group removes some vanilla spawns for each biome but this can be turned off in the group config too (such as MountainMobs.cfg). There have been some spawning issues in the past but they have been fixed in recent releases, I run a 24/7 server with the latest release and mob spawning is pretty balanced, other mob related mods could alter the balance a bit though. I'll run some tests on dungeon spawners, but again, it's all thrown over to vanilla code where it's no longer in my hands.
Another thing to note is that in recent versions, easy difficulty makes the mobs significantly weaker (each stat reduction can be configured in the config too, per difficulty for every mob and even on a per mob basis). Hard difficulty is significantly harder now though too, mobs don't just do more damage but they also move and attack faster, again this is configurable though. Normal is balanced for people fairly adept at Minecraft, Easy is for those starting out or new to the mobs, Hard is designed to make the mobs very dangerous and the world very hostile, less about building and all about survival, but all is configurable. I used to run my server on Hard as Normal just wasn't challenging enough with a lot of modded weapons and armor, but with the new difficulty updates it runs on Normal now as hard mode was too hard for most players which is the idea.
