Another view; We were in a small club and a big club. The one thing I don't have to worry about anymore are numbers. We sweated through head counts at the smaller club to see if we had enough for a 11 v 11 team. If a few kids bailed the team would fall apart. Had that happen a 2 different small clubs. The best was a parent team manager who told all the parents that that they had enough for a team but secretly took her daughter and a group of her friends to another club. The team collapsed. With the big club, I know there will be numbers for multiple teams at that age bracket. Also, the parental influence is not as great at the big club.
It is absolutely crazy to me that if you're not in the best training by 12 you are already behind for college! Oh, well - live and learn! Our club is not that small - they field at least 2 teams in every age group but the coaching is volunteers - well intended volunteers but it's hit or miss. We are seeing a big difference in the way the bigger clubs with paid trainers run practices, drills, etc. Also true about parental influence in the smaller club.
In that case I would say it doesn't hurt at all to try out for the bigger club, and keep in mind that things can change very quickly at that age as different kids mature at different rates (physically and mentally), and some kids start to lose interest. Maybe your kid might start out C team, but that doesn't necessarily mean he'd be there for long if he's good enough and is that dedicated to the game. And speaking to another comment, I've never heard of jr. high soccer, is that really a thing some places?
We have Jr High soccer. Played in the Spring and most clubs have no problem letting the girls play in both.
Jr High Soccer here - private schools play in the fall (2 practices/games week, T/W/Th), Public schools play in the spring (3 practices or 2game/1practice week, T/W/Th), the Diocese league is fall and spring (2 practices weeknights, Sat morning games). Makes coaching the u13-15s challenging for community clubs, rarely get a full team at practice until mid-May if you put any thought into trying not to overtrain.