IMO, they each have their advantages and their disadvantages, when it comes to ship building.
SE has more of "hard sci-fi" feel, has fewer options overall when it comes to design, and the greebling is already built in. OTOH, it has a ton of technical blocks, like hinges, pistons, rotors, as well as scripting language, in addition to its sensor logic. It's also a engineering game first, and a "survival" game a distant second.
EGS has more of a space opera feel, it has a lot more options when it comes to design, those options make for some great greebling opportunities. Sadly, it doesn't have technical blocks, and while it does have some logical gates attached to its sensor logic, it doesn't take it to the level that SE does. It's a survival game first, with a great ship and base building system included.
edit:
As for the graphics themselves, I personally think the graphics overall are better in EGS, but the character models are definitely better in SE. YMMV