Okay here's the deal. Before I quit in 2010 my Monk was fully merited.
H2H, evasion, STR, all that jazz.
My tier II merits were 5/5 Penance, 4/5 Invigorate and 1/5 Formless Strikes.
After coming back I've been told by some linkshell people that this is all wrong now. That the best setup is 5/5 Invigorate and 5/5 Formless strikes. That sort of rubs me a bit wrong.
You are oh so right, and the people who told you otherwise are fools. FWIW, your choices are still the standard.
5/5 Penance is the one absolute in Tier II MNK merits. Cutting down TP moves is fantastic, period, and has practical benefit in tons of common situations. Every NM you fight, any Abyssea mob where you want to reduce TP moves to get procs, any mob with a nasty TP move that you'd like to reduce... it's just so, so useful. And a short timer too.
I personally was set up exactly like you in 2010, but after using Formless Strikes nearly never, I dropped it altogether to go 5/5 Invigorate for occasional solo play. I haven't missed it Formless a bit. YMMV with Invigorate, since if you're always with healers it's maybe less of a benefit. But if you ever solo things or have thin mage support, it's a pretty healthy chunk of Regen. But really the only reason to go 5/5 Formless is if you were completely convinced you'd always have mages cure-spamming or casting regen on you, thus making Invigorate useless.
I do not find gimpy non-physical damage on a 10min timer JA very practical. I guess you could pop it for the occasional use against physical resistant mobs, or Invincible. But it's not going to make or break anything, ever.