A quick check on counters needed on rare missions that reward "useful stuff" (i.e. legendary stones, epic items, raid loot) from wowhead.
Deadly Minions: 35
Timed Battle: 32
Wild Aggro: 29
Massive Strike: 29
Danger Zone: 29
Powerful Spell: 28
Group Damage: 26
Minion Swarms: 20
Magic Debuff: 16
That list should be useful in helping to determine what followers should be more important to gear than others, and which one might be a candidate for rerolling if you get a reroll mission. Note that the really important missions (legendary stones/highmaul raids) all require 6 counters with 3 followers allowed, so you'll need the right mix of epic followers to maximize your chances (and yes, a Timed Battle/Deadly Minion follower is probably the best follower you're ever going to get). All raid missions have wildly different mixes (depending on which highmaul boss is present), so you're probably never going to have every mission at 100%. Mission Planner is your best friend (that and a level 3 barracks for 24 max level followers and one token mascot with Magic Debuff)