So the initial configuration is as follows:

EnderDragon

• needs 4 End Crystals per dragon spawned
• takes 10 minutes to spawn
• mass upgrades go from 1->2->4->6 (should be the same as Wither! 1->2->3->4)
• rate upgrades go from 12000->9000->8400->6000 ticks (10min, 7.5min, 7min, 5min)
• maxed out with fixed mass upgrade would give 4 EnderDragons every 4 minutes

Wither

• needs 4 soul sand and 3 wither skelly heads per Wither spawned
• takes 1 minute to spawn
• mass upgrade go from 1->2->3->4
• rate upgrades go from 1200->900->840->600 ticks (1min, 45sec, 42sec, 30sec)
• maxed out with fixed mass upgrade would give 4 Wither every 30 seconds

Ignoring any power costs at the moment I plan to:

General
-> rate upgrade 20%,35%,50% (currently it is 20%, 30%, 50%)

EnderDragon
-> fix mass upgrade to 1->2->3->4

WitherBoss
-> fix spawn time to 6000 ticks (5 minutes) => maxed out would be 4 Wither every 2.5 minutes)