An eidolon wanders around as the shifted form all the time as well. Whatever defenses you have on the wanering around form are at the same tradeoff as an eidolon with them. If you wantto drop that defense for more offense, it takes the action still, so there is a cost. Even at 20th level you can't afford every defense boost at the same time, so you can't even try walking around in a full defensive mode then shift to combat mode when combat starts. Druids can walk around shapeshifted constantly, eidolons are always combat ready, fighters walk around in full armour, why should the shapeshifter spend actions to ready themselves for combat?

I don't understand what you mean about the skills. They have a very limited list of skills they can boost, none of them skill monkey skills. it is a very high level before they can boost their dex to a +6, which would put them on par with a skill monkey who put no other effort into it, assuming you started with as much dex as them, and only at the very highest levels will they have the slightest bonus over them. they have very poor skills known, so a skill monkey will have more skills to monkey with. I specifically removed the "gain +8 skills" for excatly this reason, except for a few that I felt would reasonable be boosted by shapeshfiting, and made that into a level scale. An eidolon would make a better skill monkey.

If you are outstripping everyone in combat potential, then that is a balance issue with summoner that is carrying over. people who have played with summoner's say that a well built fighter is still better than the eidolon. Your advantage over an eidilon is in flexibility, not raw power. In fact, you are a bit behind, since a summoner will be buffing the eidolon all over the place. Also note that I did not give shapeshifter the base +2 NA that an eidolon gets from its base form. So in a straight up fight between a summoner+eidolon and a shapeshifter, the shapeshifter will lose. If it actually is better than everything else, then that is an adjustment that needs to be made to summoner, and shapeshifter, being based on it, would be similarly fixed.