As others have said, Marriott's resorts are a bit more upscale with a higher resale price tag and higher maint fees to match. Both have many resorts in very desirable destinations. Both have many resorts with family-friendly amenities, such as pool slides, mini-golf, activities, etc., and some resorts that are more location- or adult-oriented. However, Marriott is generally full weeks, traded through II whenever you want to vacation anywhere or anytime outside of your owned week. Wyndham FSP points may be used to internally reserve varying (room size/length of stay) vacations at any resort in the entire system - far more flexible. Wyndham FSP points are best used internally year-round, with occasional RCI trades when you don't need prime season. Above all, I'd look at the resort destination maps or lists on the Marriott and Wyndham vacation ownership websites. If you see most of the places on your wish list, go with that system and you'll probably be more satisfied with your ownership.
We sold our Marriott week because we found the maint fees to be too high for us, especially after adding the exchange fee (subject to increases too). Trading to other Marriotts for full weeks through II was too uncertain and we prefer to use cheaper weeks for the uncertainty of trading. We didn't mind losing Marriott preference in trading since we've had such great vacations in so many non-Marriott resorts. But YMMV.
We love our Wyndham points because reserving exactly what we want (different resorts, room sizes and lengths of stay each time) is easier, more certain at 10 months out and the costs are lower. We live in the southeast and we like it that so many Wyndham resorts are within a day's drive and that they usually have an indoor pool - great with kids, when weather is not great for outdoor swimming, and not that common in timesharing. If you'd reserve a lot of short stays with Wyndham or if you change your plans a lot, there can be added fees and they can stack up. For how we use it, we rarely pay added fees. Marriott has some added fees too, like for locking off a unit or using points. Much depends on how you would use the timeshare, what you want vs. what others enjoy.
There are options for using either Wyndham (PlusPartners) or Marriott (Rewards) to book hotel stays, airfare, rental cars or cruises with points, if you have this particular option with your ownership. Not every ownership with either company has this. However, alternative methods of getting a nice hotel stay, decent airfare, cheap rental car or discount cruises are usually a better value than using timeshare points of any kind, IMO. If you wanted to do this, you really have to learn how to work the individual system and accept those limitations. It's just an option when your points would otherwise go unused. HTH.