Thugs/traps will be a pain early on until you get decent debuffs because that heal is annoying. Also thugs do a lot of kb which is bad for traps. Healer bots have ok heals but all the stacked defense with healers plus ffg is win.
I would much rather go thugs with dark, pain or storm. In fact I have a 50 thug/dark and a 50 thug/storm 
.
Both bots and thugs have lots of knock back, pretty similar amounts. I've got both, and really its not a big problem. If it turns out to really annoy you, electric fences from Mu mastery is -kb and works like a charm its never bothered me much honestly.
You just cannot go wrong with either choice, they are both incredibly powerful. Honestly, go for what you like, both sets can solo avs or just about anything.
Bots/Traps is fun. The Guardian Bots combo nicely w/ Traps.
I've never done Thugs/Traps, but seems like it would be alright.
Thugs/traps has the option to double stack the pet auras giving your pets 10% BASE def, and 20% resistance to everything. Stacked with the enforcers leadership like powers, AND FFG means you have some pretty durable pets. Downside is that the MM itself isn't too durable.
Bot/traps only has the option to have 1 each of the pet auras, giving 5% def, and 10% resistance, BUT the force shield the protector bots provide gives more defense then the enforcers (but you have a cast time, and a duration, where the enforcers is automatic) AND they benefit the mastermind as well, allowing the mastermind to be pretty durable in his own right.
Basically for PvP, go bot/traps, as people are going to focus on YOU and not your pets.
For PvE go thug/traps as NPCs are more likely to go after your PETS and not you.
With Thugs/Traps you can be pretty durable if you pick the right powers. My Thugs/Traps softcaps S/L DEF and S/L RES. These builds can be pretty flexible.
I'm leveling both and so far, bots/traps "feels" weaker to me. It also seems like it takes longer to kill the mobs. I was hoping that bots/traps was good in pvp because it's nonetheless more fun to play one that thugs/traps - because I role play on my bots.
I know, i know, not much role playing goes on in coh these days but that's also why it's more fun.
Well, Bots/Traps does a bit less damage than Thugs/Traps. Thats a fact really, but Bots/ have their tricks to ramp up the hurt. For example, the assault bots burn patches can be really evil -- holding the enemy inside a burn patch with something like Mu Master/Electric Shackles can really burn even strong mobs down pretty well.
Bots/Traps is the classic AV Soloing MM, so it really can do some mean damage, but its "up front" damage isn't as much, its a bit more involved... but then they are very solid pets that can absorb damage better than Thugs. Thugs general lack of resistances means they get one shotted more often, and maintenance of their health is up to you.
Both Thugs/Traps and Bots/Traps are so powerful, even in the end-game, that for me deciding which one is better is almost impossible. A bit more damage, or a bit more survivability.. you just can't go wrong really.
I know this isn't an option you've listed, but if you're looking for an AV-Killer Thugs/Poison rocks.
Yea, I think it's going to be a very long time before I level another /pnz toon. Thanks for the suggestion though. I know how deadly poison is.
Please help me decide. I feel that thugs would be more damaging allowing me to kill faster (especially in pvp) but bots would be more survivable and so it's a tough choice.
I'm just trying to find another mm that I can enjoy through like about 40 levels (which is usually the time I start another toon).