I strongly recommend the multiple windows approach. With MDI you toss a lot of the window manager's functionality out the (ahem) window.

Often you have a couple editor windows, with their tool windows, and some documents/images you're looking at for reference. With MDI all have the same Z order, and usually a large grey box behind them all, so you have to shuffle things around lest an editor or tool window you're not even using cover up your reference document.

If you want to duplicate something from a screenshot, you can just place the editor window right overtop of the screenshot and turn it semi-transparent. With MDI you often can't do this, at least not to individual windows.

To find a particular window you have to first bring up the master window from the taskbar, then bring up the specific window from whatever method the program provides. You (at best) double the amount of time and number of clicks needed to find a window, and the second step is different for each program.

All of the windows are constrained to a box, which basically prevents you from using the program on multiple screens. Dual-screen setups are becoming increasingly common and some people have even 5-6 monitors, and/or the visible area is not a single rectangle (especially if one of the screens is a laptop, TV, etc). Even if you can extend that box across both screens, you end up with a lot of unused space covering all your other windows.

MDI is basically poorly re-implementing the window manager and taskbar on top of the existing window manager and taskbar. Leave it to the WM to do its job just as the user wants, rather than trying to force your own methods on users and breaking a lot of functionality in the process. Taskbar clutter is easily solved: place the taskbar at the side of the screen and look at how many buttons now fit on it. Modern taskbars can also group windows automatically so that your several editor windows collapse into a single menu, eliminating this problem entirely.

Heck, here's some actual use cases. Suppose I'm using these images as a reference as I design my level:

Active windows clearly visible, everything accessible with one click on the taskbar.

Mock MDI. Can't see a goddamn thing through the clutter of all these toolwindows I'm not actually using at the moment, and a box in the way behind them. The web browser and terminals aren't doing anything, but if I wanted to put some of my tool windows over there, I'd have to make the boxes even bigger and cover up all that space, or move everything into that little area. Either way slows down access to those if I do want them, since now I have to find them in the taskbar instead of just clicking a visible region - and then if I want to look at the editor and the browser at the same time, I need to move and resize and rearrange it all again.

MDI died long ago, for very good reasons.

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