Been doing some research on these forums about upgrading the prop on a trolling motor.  I've read on here about the Ninja model and the GOAT. I've seen some Minnkota models in store too. Is the advantage just gets through grass and weeds better? Can I get a little help here?

That's what they are made for.  If you fish through lily pads and grass, etc, they are golden.

They are slower in open water but the only time the slowness comes into play is if you are chasing schooling fish breaking the water or using the TM to move between spots. 

I keep a Ninja in my boat and use it when needed, but keep the two blade on most of the time. There are only a couple of places I fish, like the St. Johns river, that needs one, and I spend most of my time fishing grass free waters, and chase a lot of schooling fish.

In some areas, I don't care what prop you have, you are still going to lose a lot of religion by the end of the day.

Hmm, what about the design makes them slower in open water? So unless I am in very "weedy" waters it would be a detriment to me? I am new to the trolling market game and just saw this option as an "upgrade" and figured it would be a good idea but from what you are saying it sounds like unless I REALLY need it it would be a bad idea.

The extra blade. Same if you change the prop on your big motor from 3 blade to 4 blade. You sacrifice in one area to benefit in another

It probably depends on the boat and size TM as much as anything.  On my 20' Javelin and 80# TM, there is a noticeable difference in top speed between the two props, that's why I keep  the two blade on it.    I've also read reviews that claim there is no difference, and some claim the three blade is actually faster, me personally have not seen those results. 

You should always keep a spare prop, sheer pin and nut, buy the three or four blade and judge for yourself.

I also use the four blade Ninja, it's definitely a lot slower but is the best in thicker junk. 

I fish the very weedy Potomac and I use a 2 blade but added the Grass Goat to the shaft.  Best of both worlds.  

I have a 3 blade with dual ninjas and it's a beast with only a 55lb motor.