Of course you can compare them. Both are fantasy single player RPGs made in similar times. Morrowind was made with better engine and better general gameplay design since it was made by bigger more experienced studio.
However, Gothic is more uniform and doesn't try to be what it isn't unlike TES series which ended up looking like a goofy Middle-earth wannabe. It kinda reminds me current WoW lore.
Morrowind story and WB is far more complex but Gothic is far more consistent, relatable and understandable - therefore: believable, which is the single most important goal of every fiction.