I don't have much objection to the existence of a second starship. Some people have suggested that any resources used to build a second starship would have more believably gone towards the primary starship, in order to increase the chances of it being completed.
Since when however do humans react rationally in a crises? I for one wouldn't be surprised if the threat of imminent death didn't cause some powers on earth to ignore the good of all for the sake of themselves ("What!? You want us to help save your lazy American butts? Screw that, we're building our own ship!").
On the other hand, maybe we could assume that Maesis was spawned from people on earth who survived the asteroid impact. A post-apocalyptic civilization might decide it wise to build one or two starships using the already-developed technology, the near-death experience having driven home their vulnerability to them.
(I don't think we know for sure just how long to people in the Conestoga were in deep sleep, the journey to another star may have taken them many dozens of traditional generations)
As for the starships meeting each other, it isn't inconceivable to me. There would be a limited number of star systems within range of earth that had a good chance of being habitable. Two sets of people both searching for the same thing are bound to cross paths eventually.
The one thing about their meeting that I don't understand is why it would be on a venus-like planet. Why would Maesis have landed there? The Conestoga passed by and rejected a number of worlds, and only landed on New Terra because it was running out of resources to continue the search.
If it turns out that the maesis landed on Cythera for no other reason than a similar resource shortage, that to me would make their meeting much less likely.
In short, for their meeting to be believable, there must have been something about Cythera that drew the colony ships there.
Another unrelated problem that I have heard stated about Maesis is that the name wasn't chosen to have any particular meaning, the developers just used it so it would sound cool. I have seen at least one person suggesting that a better name should be chosen, one that has some sort of appropriate background meaning.