Having only played a few months now, I don't have the experience to make a call on many of the top alliances so I'll just go with the ones I have had experience with.
Its more fair to judge alliances based on their size. Clearly any noob can form a massive MRA so lets not ignore those who have chosen to remain smaller.
LARGE ALLIANCES: (300+)
Hawkesy: EOW are aggressive and out to prove themselves. Their offense to defense ratio is as good as any of the alliances they are fighting. I think they got a little soft from beating up on noob alliances, but they will learn quickly and improve their tactics to give a challenge to more worthy foes.
Horod73: Might be the best diplomat on Alpha. ECLIPSE is a widely dispersed alliance all over the map & considered by many to be an MRA, yet has managed to remain largely at peace with neighbors. Please teach me your tricks!
MID-SIZED ALLIANCES: (100-300)
Clamenza: The Gemini Order is scary. They have a wicked offense/defense ratio, got slave alliances all over the place, and scariest of all is no one really knows where they stand in the scheme of it all.
Sch0lar: While there is debate as to his skill as a player, his skill as an alliance administrator can not reasonably be questioned. I think Orthia is more active and ambitious than TW. Maybe one day they will decide to prove it.
SMALL ALLIANCES: (100 or less)
Phish - Island League has a 5:1 offense to defense ratio and has more than held its over against the Thunder Gods.
Op.Ivy - With only 16 members, TMOAE is the epitome of tight-knit alliances. Any who intrude on their domain, from TW to Orthia get their o-rings blown out.
WORST ALLIANCE LEADER: Any who would let Toast be a member