Let's see some more pictures. I JUST got done pruning 2 Japanese maples in the landscape for a customer, less than an hour ago. You can see how the branches near the top are growing more robustly than those at the bottom because they are becoming heavier. You're going to have to restrain the tree if you want to keep the lower branches. If you don't, shedding is inevitable as the tree tries its best to grow tall/wide. I'd remove the crossing branch w/o hesitation, then I'd start looking for ways to restrain the top with an eye toward increasing ramification (branch density). It's really difficult to try to explain how to prune containerized Acers without being able to point & explain, but I'll try. In your 'Y + 1' way of describing the growth habit, you should be concentrating on removing either a leg of the Y or the central branch extension. Your eye will tell you which is the best to remove, and your eye will decide by the direction the tree will be growing after you make the cut. IOW, you want the branches to be headed in a favorable direction instead of into trouble, where they interfere with other branches or the natural path of other branches. Cut back the top 1/3 of the plant very hard. You will, in most cases, want to remove the central leader back to a fine pair of branches, then remove the central leaders from those branches, and even do it again, if required. All branches in the top 1/3 of the tree should have only 1 pair of buds on it, and as the tree back-buds in inopportune places, you should rub the unwanted buds off. Be a little less aggressive in the middle 1/3 of the tree, and prune only enough to keep the tree in bounds on the bottom 1/3. It's best to start this type of pruning & pinching when the tree is very young, but you can do it now with no problem. I can't be more specific because I'm not getting a good look at the tree, but that's how experienced bonsai practitioners keep branching well ramified yet delicate, instead of heavy. Honestly, that tree could easily have 60% of the canopy removed, most of it near the top, and still be a very attractive tree by mid summer. The important consideration is that as you build branch density, you decrease internode length and provide yourself with myriad pruning opportunities that virtually ensure your ability to build an attractive framework. Notice how hard I'm working to keep the top restrained while bottom branches develop: Al

The root balls on JMs are not very big. I have known people dig and move them 100s of miles while they are in full leaf. If you get 2 of the 24 inch, plastic plant "saucers", that stand about 18" tall, you should be able to dig the JMs (dig at least as wide as the drip line, and then make adjustmments as the root ball is made evident) and put them in the pots with no problems. If you need to trim a few roots to make them fit properly, it should still not be a problem. Keep them in part shade (at the least, afternoon shade) and water them well, waiting for the top couple of inches of soil to dry before watering again, and they should be fine. Don't feed them. If you can't find the wide planters, then any LARGE pot should do. Ask at your local nursery or at a landscaper for a 7 or 15 gallon nursery pot - you may have to pay for them, or they may give them to you. If you use a 15 gal., then put a large garbage bag of styrofoam peanuts in the bottom to take up space - the more dirt there is, that the roots don't/won't fill up, the greater chance of rot setting in. Adjust the amount of "fill" according to the tree's root ball size/depth.

By no means an expert here, but i agree with dredawg re the arborvitaes. To me they appear too large for their position above the brick wall. Also I don't think trying to limb the jm up enough to be a canopy for the arborvitaes would work. When you replace the arbor, could you modify the design so that the jm doesn't encroach into the frame? I can't tell from the pics, but maybe it would look fine for the jm to extend into the patio area (if it's not interfering with the table and chairs) if the arbor frame wasn't there to emphasize the issue. You can do some pruning to control branches extending out further than desired. But I would visualize the ultimate allowable width of the jm with its expected height and see if that works aesthetically.

Thanks for that Jalcon Have seen this post before I think with a lot of these Situations the Choice of to Prune or not to Prune is in the hands of the Tree owner whether Purist ~ None Purist or Experimentalist I myself with this Tree have decided to remove the bottom 2 Branches before the Tree becomes too Branch Wound Envisaging what the Tree would look like with just a single Curved Trunk I would consider this the best Option,(In My Opinion as a Comparitive Beginner to many on the Gardenweb) Best wishes Stephen,Cheshire,UK