The Reapers were, indeed, the central antagonist in ME3. They were there at Tuchanka. They were present in the geth during Rannoch, which included an actual on-foot boss battle with a Reaper. Their tech coursed through Cerberus' veins every step of the way. And they're the reason why we're building the Crucible in the first place, and gathering forces to stall their advances while it's under construction.
While I do agree with the fact that the reapers appear at tuchanka, rannoch and are the basis for the crucible those are story elements - not really the game play elements.
From a gameplay perspective the reapers, as themikefest pointed out, have only one more core mission more than cerberus. I actually did have a breakdown of EVERY quest in ME3 by foe and by type (foe = Cerberus, Reapers, Cat5, and X for Fetch and Type==Main, Side, and Fetch) and in that review, I found that cerberus is way ahead of the reapers. Even in core missions (eg JUST priority missions) we see:
Prologue: Earth - Reap
Priority: Mars - Cerb
Priority: The Citadel I - NA
Priority: Palaven - Reap
Priority: Sur'Kesh - Cerb
Priority: Tuchanka Reap
Priority: The Citadel II - Cerb
Priority: Perseus Veil - NA
Priority: Geth Dreadnought - Geth
Priority: Rannoch - Geth/Reap*
Priority: The Citadel III - NA
Priority: Thessia - Reap
Priority: Horizon - Reap
Priority: Cerberus Headquarters - Cerb
Priority: Earth - Reap/TIM
*= I will count this as a Reaper mission, even though you are fighting reaper controlled geth, it is still a reaper that controls them and you take a reaper down in the end.
Total
Reap = 7
Cerb = 4
Geth = 1 (technically 2 but that one counts to the reapers)
http://masseffect.wi..._Effect_3_Guide
The reapers lead, but by a small margin. And these are JUST priority missions. These are the main missions which dictate the flow of the story, side missions just dictate some character deaths or character development. And look, even in the priority missions cerberus is closing in on the reapers by 3 missions.
It is like I said. The story says "reaper reapers reapers" but the game and the game play goes "Cerberus Cerberus Cerberus"
What do you think speaks louder, actions or words?
That there'd probably be a pretty good reason for clashing with Cerberus as a diversion instead of getting thoroughly blitzed by the Reapers in head-on confrontations. BioWare already did it once with the Collectors.
I know...that part in ME2 never really made any sense to me though I always thought that the merc fighting would actually lead to something lol. Like, we are told again and again "Collectors Collectors Collectors" and we spend the majority of ME2 just shooting Mercs and solving personal problems...
I never did a count of ME2 missions but lets see:
NAME FOE
Prologue: Save Joker - Collector
Prologue: Awakening - NA
Freedom's Progress - Mechs
Dossier: The Professor - Mordin Merc
Dossier: Archangel - Garrus Merc
Dossier: The Convict - Jack Merc (I know it is guards but it technically will be counted as mercs for sanity)
Dossier: The Warlord - Grunt Merc
NOTE: you need to complete these dossiers to continue the game
http://masseffect.wi...t_1_Progression
Horizon Collector
Reaper IFF - Legion Reaper
Collector Ship - Collector
Reaper IFF - Crew Abduct Collector
Can be done right after the crew is abducted
http://masseffect.wi...ession_Missions
The Normandy Attacked - Collector*
Collector Base: Infiltration - Collector*
Collector Base: The Long Walk - Collector*
Final Battle - Collector*
*=All really the final battle mission, so I count as one instance
http://masseffect.wi..._Effect_2_Guide
Note, these are JUST the missions that drive the story. Most of the recruitment options in ME2 are OPTIONAL - save Legion and the first four.
So, just looking at this...we can see
Collector = 6
Merc= 4
Reaper = 1
Mech/Robot = 1
My god...the Collectors are dominant, but lead by a marvel of two missions (vs the three that the reapers lead by in ME3). I won't do an analysis of all of ME2 to find which missions are more merc vs collector because we all know the result of that. So it seems ME3 just copy/pasted ME2s villain formula.
Here is the breakdown of ME1
Mission FOE
Prologue: On the Normandy NA
Prologue: Find the Beacon Geth
Citadel: Expose Saren Thugs
Citadel: Garrus Thugs
Citadel: Shadow Broker Thugs
Find Liara T'Soni Geth
Feros: Geth Attack Geth/Thorian
Noveria: Geth Interest Geth/Rachni
Virmire: Assault Geth
Ilos: Find the Conduit Geth
Race Against Time: Final Battle Geth/Krogan
Total
Geth = 7
Thug = 3
Rachni = 1
Thorian = 1
Looks like ME1 did it right at least for primary missions.
Again. it comes down to actions vs words or more importantly. Story vs Game play.
If the story tells you Reapers Reapers Reapers and the game has you fighting Cerberus Cerberus Cerberus. What are you suppose to think? Actions are louder than words.