what is your goal, and how will you play?
the usual sheep will say poison or dark and they are pretty off base if your goal is to solo av's and gm's or to make your pets as unkillable as possible.
dark has it's uses and is excellent in teams, however the heal requires your pets to all be in melee range of the target. this is not always ideal. properly playing thugs to it's maximum potential means at least three keybinds dedicated to goto for each tier to keep the ranged guys ranged and the bruiser in melee. stacking tar patch is noticeable increase damage for your thugs, but this is not the only source and many mobs will run out of it especially av's and gm's that can't be rooted. thugs/dark does work, but it's far from optimal
same deal with thugs/poison. while is has good debuffs (not the best, good) you will be replacing pets often and you need a bit of recharge to get the anchor ability perma.
the two ideal, best secondaries are traps and time. here is why:
with traps and time you can softcap your pets defensively. two defensive io's in enforcers gives your pets 20% def to all. ffg and farsight give another 15%. two slot gangwar and put edict of the master and call to arms +5% def auras and voila - your pets are pve softcapped. with powerboost you only need one of those +def auras. that's before you add in maneuvers. this is actually superior to bots, as the bots bubbles are not up 100% of the time and the lt pets only get one bubble each.
with traps you can:
lock runners in place, even av's. darkest night an av or gm? they run off. have fun!
soft control in caltrops but don't bother slotting damage proc io's anymore. they don't work like they did on live with the new ppm mechanic.
with enough recharge a pretty hefty pbaoe stacking +regen aura, but useless until later levels
stacking -20% def -20% resist that is effectively perma
the only actual total shutdown of all regen in the game. poison trap is only a -1000% regen for masterminds traps. on other at's it doesn't have -regen.
poison trap also is an occasional hard and soft control, with an actual hold proc for minions and lt's and a barfing animation forced on av's and even gm's.
mezz protection. malta can stun you for 40 seconds at a time. the right arachnos pack you will be perma held/slept/stunned if you aren't keeping break frees handy for EACH PACK
some of the hardest content to do while you level is villain side even when you keep them to EB level. one of the arachnid story arcs has you fight biff. all arachnids have massive regen. massive. biff is even worse. my necro/dark couldn't break it because howling twilight and twilights' grasp even stacked was not enough -regen. after 30 minutes i pretty much just alt+f4. but thugs/traps? it was a 4 minute fight and nobody took a hit.
When a power says -50% regen, it's actually only a 5% reduction in the targets regen rate. There is no power like mm poison trap. it is actually quite overpowered in the right hands and with enough recharge is up for every pack. if you use super speed or some stealth you can jump into a pack and drop it and negate the alpha entirely, even from the boss.
time ticks nearly all of the same boxes above. it does not have mezz protection. it does not have as much -regen (spamming time crawl and the hold gets you -300%, on par with dark but also a HOLD) and would have the same issues with +2 eb biff as a thugs/dark would. what it does have is a pbaoe heal that in total heals as much as twilights grasp. it has farsight which when powerboosted is +20% def all to you and your team and pets which actually allows YOU to softcap pve smash/lethal or even positional with some slotting choices. it has a slow patch like caltrops that does no damage but can hold minions and lt's randomly. chrono shift can help with end to a degree but does not substitute slotting end in your pets and it has a pbaoe -tohit aura you run that really helps (until you get mezzed).
when choosing between the above it comes down to this - traps is better solo, but poor on a team. it works best if you have team teleport to move everyone around and keep them in the ffg and can get quite spammy, but i killed a +2 av at level 29 as thugs/traps and only had to replace the arsonist a couple times because poison trap shuts down all regen, period. traps is not fun in a team.
time is great solo because your pets don't need to be within a bubble to be softcapped but the lack of mezz protection has killed me and them a lot. it is however superior for teaming due to farsight, chrono shift, your hold, your slow patch. time also has -20% def and -20% resist aoe but will take some effort to make perma and unlike acid mortar which you can have two of and they stack as far as i can tell slowed response does not stack on itself.
bots/time can actually softcap you the player to incarnate level defense, but bots does not do anywhere near the damage of thugs and no, i never count gang war.