First of all I would worry if we gonna see the full gen II someday xD.
I share your feelings here, but I have always thought that CP is not a good way to measure a mon, if the games stays at it is now, without pvp, CP means nothing, the AI of the gyms are way too easy to predict, so even with legendaries, or 5k+ CP mons that does not mean anything to me, it will take maybe 10-15 more seconds to kill that 5k cp mon with my vaporeon,my dragonite or my alakazam, probably even less, everything is subjective.
You can state that placement is gyms is the most important thing, I don't share this feeling, I won't say is totally useless but in my experience around 99% of the times someone attacks a gym he/she takes the hole gym down, does not matter if the 3 last mons are 3,5k or 5k, it will give them just a bit more time or probably use 2/3 more potions and revives, nothing more.
And even if they leave the last 3 mons for example, in a matter of minutes/one hour another person will take the rest of it down.
So I think we don't have to worry of those "big mons", by the time they come (at this speed we gonna get gen III on a year from now) they will have balanced it someway for sure, for example a buff to fight quick moves and a machamp with 2,2k will melt that 5k slaking in a matter of seconds.