Unity 5.0 general FPS issues.

I've seen a lot of threads about the editor FPS being low, and I understand that the editor is exceptionally terrible at FPS. I do see a drastic improvement on the standalone build, but not as much as I would expect for near-empty scenes compared to U4.6.

In unity 4.6, I would see 200-300 FPS in basic scenes like my menu screen, empty unpopulated levels, etc. However, I can't seem to break 100 in Unity 5.1.1f. In my playtest level (a single 2-poly plane scaled up with a few scattered objects like lights and breakables) I got around 150 fps standalone, 100 fps editor, and in unity 5 I get about 40 fps standalone and 20 fps editor.

Now the real issues come in when I try to add a few object to my scene.
I have a script that takes a 2-color image file. Black for nothing, white for room. It then iterates through the image and generates a map based on this from a prefab "room" that is made up of simple geometry (2-poly plane for the floor, boxes for the walls/corners).

The script is set to "waitforseconds" of 0.001. At the beginning of iteration, it generates ridiculously fast, however about 1/3 of the way through this 32x32 map image, it drops in speed, noticeably slowing down from about 70 fps to ending the script at 20 fps. Once the script ends with the image, it sends a broadcast to all its new child-rooms to "enter phase two" which each room then deletes (as a one time function) all walls adjacent to another room, thus creating larger rooms and hallways. Again, in 4.6, I go from 200 fps to about 100 fps, then back to 200 fps when it's done. In Unity 5, however, I start at about 70 dps, end at about 20 fps, then pop up to about 30 fps when it's done.