Hi there! If you're son wants a deck, there's quite a few options open to him from the cards you've listed.
One of the best decks in the format is M Mewtwo, however, this is talking about M Mewtwo Y, not X. It's a good competitive deck as well as a beginner deck because the strategy's pretty straight forward. Attach an energy to do more damage, and then throw in a couple support pokemon, usually Garbodor.
A deck that's not quite popular, yet has potential as a rogue deck is M Venusaur, mainly the one from Evolutions. This is because the recent release of its spirit link. Its got a hefty attack that requires a bit more support than M Mewtwo, but still has a decent reward for investing into it.
M Sceptile is a gimmicky deck, that although has a hard time against the top decks in the format, can do well and be fun to play on a beginner level. The main strategy is to heal Pokemon that have a lot of damage on them using M Sceptile's Jagged Saber and deny your opponent prizes.
You could also try M Pidgeot, which is a deck that's pretty versatile due to its colourless typing. I don't really know much about the deck, but I do know that it's not a bad one.
Those are the competitive/ semi-competitive decks you could try building. For non competitive decks, you can pretty much throw anything together. I think that for a start, two types (not including colourless) would be good, so Xerneas, M Mawile, Goodra and Pidgeot would be fine. Some cards off the top of my head that are great for beginner play are Tierno, Shauna, Professor Sycamore, VS Seeker, Ultra Ball, Great Ball, Professor Birch's Observations, Roller Skates, N and Giovanni's Scheme. All these cards help to obtain resources and because most beginners don't usually start off with full blown strategies, having these cards in your deck can help win against other beginners. Now, with each type there are cards that provide advantages. For fairy, water and colourless, some good cards are Fairy Garden (Free retreat to those with Fairy energy attached), Fairy Drop (heals damage to a Pokemon with a Fairy energy attached) and double colourless energy (two colourless energy in one card). There are cards that are useful to water types, however those mainly affect typing, not Energy cost, so they're not that useful in this deck. If you want to add some Pokemon to this deck, Articuno AT and Regice AOR are some good water types.
Also, if building a deck is too hectic, you can always just buy a starter deck. These are prepared decks that are meant for beginner play. There are also Battle Arena decks. These range somewhere between competitive level and a beginner level. They also have a lot of staple cards in them, which can serve as a nice starting point. What's more is that there are two of them, so you can play with your son if you get this.
Be sure to check out the Deck Garage for examples of decks other people are playing as well as to receive help on any decks you post there as well. If you post a deck list there I'm sure there will be others willing to help you out with that.
Hope this helps!
