Big megapixel is fine. Unfortunately it comes with:
Slower performance (fps, file transfer, editing)
More high ISO noise
High storage space consumption
The problem is how will it look good compared to the D800?
If they are aiming to trump the D800 on MP that could mean as you say, really large files, but poor body performance. The D800 manages 5fps and 6fps modes which makes it more than just a pure studio/landscape cam. It has tons of DR.
How will a Canon at say 42MP with say 3fps and no fast crop modes (since Canon doesn't do that, why?, who knows, just because), probably 1.5-3 stops worse dynamic range, probably no cropped video mode so we are back to moire/aliasing again (since Canon doesn't do cropped 1920x1080 video modes for the most part, why?, just because) for $1500-2000 more than a D800 sell? Even at the same price you'd be giving up fps and DR all jsut for 6 more MP? What do you get? Sluggish performance compared to what the D800 can do in 1.2x and 1.5x modes. Much less dynamic range (unless Canon for some silly reason held the good stuff back from the 5D3). Are 6MP, once you are so high already as 36MP worth $1500-2000 more at the cost of everything else?? I don't see that other than for a very select subset of landscape and some studio people where every last bit of resolution matters more than anything, more than even DR. How can they charge the price talked about in the rumor?
I'd rather hear them talk about close or near to D800 resolution but increasing the DR and keeping the 5D3 body performance, 6fps (at the absolute least in crop modes, but if the speed only comes in the crop modes, then again how do you sell it for anything more than the 5D3 when it is then basically just the D800 but a year later? maybe if they go to town with the video I guess.).
The real problem is simply that they didn't fix up the 5D3 low ISO DR (and give it a sharp 1.6x crop 2x2 c30-like sampled video mode), they talked about keeping MP low to focus on other IQ aspects only they didn't seem to succeed and ended up with worse low ISO IQ than the higher MP cams, if they had just done that, fixed up the low ISO DR, then you'd have had a real all round camera, nice 6fps even at FF, top AF, good low ISO DR to give landscape shots a boost compared to the 5D2, only reach for wildlife would be missing and that might come in the 5D4 in a few years. Without the DR boost though they left the landscape shooter not getting a lot compared to the 5D2. It's still a very, very good all around camera, but they did leave the gaping hole of not one thing better for low ISO stills, slow shooting.
Anyway it seems hard to see how they will charge closer to 1DX pricing for this with the D800 hanging out there if it will just be some slow camera with 40MP and nothing more to it. I'd aim the MP a bit to the lower side of high and maintain the body performance myself and focus on dynamic range too.
I'd take the 5D3 in a second over a 3D that was 40MP, 3fps, had the same DR as the 5D3.