On a serious note, any chance you can post a diagram of the basement? Even if it is just hand drawn. I'm looking at the sideways pics, and still can't get a good feel for what you are working with.
Our basement was unfinished when we built the house, but we stubbed in for a wet bar and a full bath. We didn't finish the basement until 4 years later, but thankfully, I got good advice on where to place the drains and it worked out well.
Given that you will no doubt want a fair sized storage area, then likely a big open living area, maybe there is a way to incorporate the shitter without moving the drains. You should have more flexibility on a basement layout than with the main living floor.
On the other hand, if you have to spend even $5,000 to move the drains (probably wouldn't be that much, but . . .), it is still a good investment in the long run to get things laid out the way you want. If you can't make it work as is, then bite the bullet and pay to have the drains moved.
Somewhat related - have you thought about what flooring you will use in the living area? We put a thin carpet in ours, glued directly to the concrete floor. Inevitably, you will get some water in the basement (sump pump failure, monsoon rains, whatever - it's going to happen). By getting a thin carpet with no padding, you can suck the water up with a wet vac, shampoo and then use air movers and de-humidifiers to dry it out. It's happened twice in our basement, and I was just able to rent some equipment at Home Depot to dry out the basement rather than making an insurance claim and dealing with that hassle (and increased insurance premiums). If you have padding and you get any significant water in your basement, you'll have to rip it all out.
We are getting ready to start a major remodel of our house. The oldest area is our basement - we finished it in 1998 and haven't done anything to it since. It has held up pretty well. The carpet needs to be replaced, but it isn't awful. Here are a few pics of Emma that I took just a few days ago that show the carpet (ignore all of the black threads laying around - she demolished a tug-of-war rope). We've had tons of parties in our basement, not to mention 3 kids and their friends, yet the carpet is still passable 22 years later.
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That being said, when we remodel the basement, I think we are going to go with stained and polished concrete for the floor, and then use several area rugs. I wouldn't hesitate to go the carpet route again. Here's a pic of the auto museum's floor, which is kind of what we will be shooting for, just a bit glossier:
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