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 vein, 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.
The game's first few levels being rather slow in comparison to how chaotic later levels (and by extension the rest of the series.) can be, makes some sense from a narrative stand point. It is established early on that Humanity was on the brink of defeat and with their only chance of salvation (The Time Lock) they had no idea how to use. It was likely that Mental's forces became careless and stingy because they figured victory was a practicality in the bag for them. But once they received word that humanity now had a way to open the Time Lock and that their best warrior (Sam himself) was going to open it, they now had good reasons to be concerned and dedicate more soldiers to the field.
