Fridge Brilliance: BFE has a (relatively) more realistic look because it's the reverse of the "cartoon-izing" that the series has gone through. The sequels got more cartoony, so a prequel would be less so.
In the same spite, a few of the enemies from older games are more effective. For example, Major Biomechanoids can sprint and fire more rockets at a time and Adult Arachnoids fire more bullets at a time and actually can dodge your rockets. Hence that, it's most likely that before the events of BFE, Mental has already thrown some of his forces to Ancient Egypt before "updating" them.