I have both, I have two MN12s and a 2000 Grand Marquis.
I have the Grand Marquis for vacations and for the daily grind taking the kids to school and all the functions having kids involves.
Issues can be similar to the later Thunderbirds, plastic intake that can split, the tranny is improved over what the thunderbirds have but still have things like TC shudder as a possibility (but over your 94 thunderbird it has a new TC with new friction material and should have Mercon V already and since factory). 98 was a redesign year, adding the watts linkage, bigger front brakes, a new look, COPs instead of coil packs, fail safe cooling. 2.73 gearing is a bummer, but the change to 3.27 would make the difference.
Lots of what the other person listed as bad is really not that bad. Having a steering box instead of rack and pinion and a full frame are not all that bad.
I miss the Grand Marquis being my daily driver. It is comfy but not sporty feeling, huge trunk if you need it, and built to take abuse and crappy roads. I would probably still have it if I didn't have kids, I like the large car and I am willing to take the difference in gas mileage to have a large car that is safe and roomy with enough trunk space for a weeks vacation for 4 people (I did add airbags to the rear to get rid of the sagging back when it is full).