Meta change?

Question 1:
No, the easy access to Vaporeon and its high CP and durability won't be changed with gen 2, and unless something more powerful gets even easier to obtain (which is unlikely), Vaporeons reign will continue.

Question 2:
I'm pretty sure that Ampharos will be better than Jolteon. Although it has slightly lower CP, it's much more durable.

Also, Lanturn is an interesting water/electric type that could be very good against Vaporeon with an electric-type moveset, as it would both have SE STAB and resist Vaporeons attacks at the same time.

Then you have Kingdra, who will double resist Vaporeon. If it gets double dragon STAB, it could be pretty good against it as well.

It's not possible to say yet whether these pokémon will be better counters than the ones currently available, but depending on the movesets they get, they definitely could be.

1) If electric and grass type pokemons and moves gets a buff, expect to see vaporeons on lower tier. If not, vaporeons will still rules most gyms.
Edit: If vaporeons and other water types have bubble in the next update, say goodbye to metas boy ( ͡° ͜ʖ ͡°)

2) Exeggutors and Venusaurs shines on fighting vaporeons on daily basis. My exeggutor can fight maximum 3 vaporeons with extreme dodging, but most of the time only 2. Venusaur in the other hand, is good but vine whip itself is weaker than exeggutors zen headbutt solely on it's dps and even with bonus stab and weakness bonus. Still can't defeat exeggutor zen headbutt with stab because of lower attack stat and slightly higher bulk.

None of this can be answered before we know wich moves each pokemon gets and how good each move turns out to be. We can make hypotesis based of the knowledge we have about the main game series, but that doesn't necesarily translates well into Pokemon go.

From a typing perspective, doesn't Houndoom counter eggsecutor?