Okay, I'm not sure why you would ever choose a size small eidolon. Especially at low levels, when your pet beasty is mostly a melee combat machine (maybe scout sometimes)...well, just compare.
Adding up bonuses and penalties, here is what you get net for a small eidolon:
+2 AC (1 from dex increase, 1 size)
+1 init (from dex)
+4 stealth (size)
-1 attack (+1 size, but -2 str loss; if you spend the feat for finesse, this becomes +2 though)
-3 damage (-2 str loss, -1 avg from smaller die size)
-1 HP per level (con loss)
-3 CMB (-2 str loss, -1 size)
-2 CMD (+1 dex gain, -2 str loss, -1 size)
Now: do those advantages really equal those losses? Because I'm not thinking so, personally.
What do people think of simply saying size small gives +2 Dex, and -2 Str? That would serve to equalize things considerably, in my view. If that's too much, I'd even take the -2 Con.
For the record, all of this is simply so that my Summoner can have a pikachu. :) Although I wish giving it Iron Tail was not so sub-optimal.
Try taking your large eidolon into a building meant for medium creatures, or into that river boat meant to take you across the river, or across that rickety bridge. It's going to be doing a lot of squeezing and sink a lot of boats unless you have reduce person (at which point you are using up resources to make up for a weakness).
I find that GMs and players alike forget just how cumbersome having a large party member can potentially be. Sure they are great in combat, but they are hilariously bad nearly everywhere else. Imagine having a diplomatic scenario, in which no one is paying any attention to the party bard, because everyone keeps staring at the scary monster towering over everyone in the back row.
Small eidolons make great messengers, flyers, scouts, spies, sabateurs, etc.--essentially any non-combat role they could likely do better.
Among other things, they will have more evolution points (4 more than a large eidolon, and 10 more than a huge one).
I do not have a problem with it being worse in combat than a size Large eidolon...because that costs points. I do have a bit of an issue with it being worse (much worse) than a size Medium one, because those cost the same. Especially when
a.) It does not (in my opinion) get enough compensatory advantages to make up for the loss of combat efficiency.
b.) physical combat is the primary purpose of an eidolon, especially at low level.
How exactly does it perform 'any non-combat role' better? Unless it involves a Stealth check (where they get +5) or a Dex-based check (where they get +1), a medium eidolon can do everything just as well as a small one (and some things better; anything that involves a Str- or Con-based check, for instance, or carrying something heavy).
As for the disadvantages of a size L eidolon...
1.) I'm not comparing to size L, but to size M (which don't have most of the disadvantages you list)
2.) You do realize that the summoner can simply dismiss his eidolon any time it would be awkward? Like boat crossings, or squeezing into buildings, or when the bard is trying his diplomacy? Unless I'm missing something, he can summon it again when he needs it (or just when he's gone through the tight door or crossed the river).
Familiars make superior scouts and messengers (for one thing, they don't lose most of their HP if they move very far from their master), and they come with the full spell power of a wizard. An eidolon is first and foremost a combat machine. It should be capable of carrying out that task effectively...no matter what size it is.
Not to mention using a small sized eidolon for a "familiar" if you're trying to fool the general populace of a town. Also, a small familiar would be far more useful to use as a wand monkey for, like, a master summoner build. Smaller, higher AC, can still have a high speed, and damage from wands/spells isn't based on size. make it fly for more hilarity.