Engineer just gives you more info, where MechJeb has some other tools like (automatically) finetuning maneuver nodes and automatically executing those nodes
I love MechJeb. I learned how to do everything it does for me manually, it's a huge time saver. Automatically planning rendezvous, plane changes and Hohmann transfers is the best. Just used the automatic landing feature yesterday, I feel like a real missions director now.
Edit: Here are some of my recent shenanigans from the last week.
Old science station:
New science station:
The lifter than put it all up there: