Generally speaking, you will achieve the best results by consolidating your sites under one domain with a dedicated folder for each country as you described. I would recommend delaying the move until you are sure your sites are not under any penalty.
The advantage you will receive with a single root domain is the consolidation of your Domain Authority. It sounds like your sites were doing well before the penalty. The higher DA can help even further.
Thanks again for your thoughts. This is actually a topic I am very involved with. I work as a Technical Director in a large digital agency and our SEO team just recommended a large Fortune 100 customer to break their web property into market ttlds from .com/de, .com/es etc into .com .es .de using the same top love root domain. According to our SEO team DA is sort of shared if the same root domain is used. However, local ttlds will obviously give you better rankings in local Google engines.
My thoughts are the right approach probably depends on the size of your brand. If its easy for you to build up quickly DA for local ttlds are preferred. If you are a smaller player you might run better consolidating everything under one umbrella to share DA.
I am actually running an experiment for one of my projects where I am doing the ttld breakout for one domain to compare organic search traffic. the benefit with local ttlds is that eventually you can tie those to market-local servers which boosts again SEO in local markets. This isn't possible for directories.
Do you share my thoughts Ryan? As said, this is a very hot topic for me at this moment.
P.S. I will definitely reach out for recommendations - thank you.