Next project

This all depends on what your goals are for your new project. I see a few options here: Are you aiming to test your knowledge or expand on it? Granted these two are always interrelated, but depending on which you are focusing will help narrow your options. Also, Do you want to start something primarily for yourself or will it be something designed for the community? This is another polarizing question that needs to be answered.

Testing your knowledge:
If your goal is to test your knowledge, then you are sticking to things that are already in the realm of what you can do, without having to spend much time learning new techniques. Obviously every project will have challenges, but this is meant more to sturdy the foundation you have already set... Projects that fall under this category are:
-My FF3us hacking project
-My hacking project ported to RPG Maker with the FFVI SDK
-My FFVI Advance editor (depending on your current level of knowledge concerning GBA)

Expanding your knowledge:
Expanding your knowledge focuses specifically on accomplishing new feats, taking on new challenges, and increasing your utility to the rest of the community (as expanding your knowledge also expands the knowledge of the whole community, assuming you stay involved). With this goal you want to avoid carbon copies and simple code translation. Things that fall primarily into this category are:
-My FF3us hacking project (assuming you have anything new added to your game)
-FFV Hacking and become a FFV specialist
-FF2us Hacking and become a specialist
-My FFVI Advance editor (depending on your current level of knowledge concerning GBA)
-Start spriting

Is this project for yourself?
Is the accomplishment entirely for your benefit? If you don't plan to share the project beyond those here and maybe a few who ask, then this project is mainly for your benefit. This is where the challenege is more important than the result because the final product may or may not be something the general public would have interest in. Bottom line, its for you! Most your options fall into this category, however there are a few that may specifically be less important for the community, those are:
-My FF3us hacking project
-My hacking project ported to RPG Maker with the FFVI SDK
-Start a Final Fantasy clone in C# (XNA development)

Is this project for the community?
This is where you put your skills to the greatest use. Here you have a project that is designed to be shared with others, to either expand everyone's knowledge or for the simple enjoyment of others. This category focuses on the appeal of the final product to the masses and includes:
-My FFVI Advance editor
-FFV Hacking and become a FFV specialist
-FF2us Hacking and become a specialist

My personal thoughts:
As you can see, your own personal FFVI project hits 3/4 categories, arguably 4 if its a good one (which id be willing to bet it will be). I always enjoy seeing what people can do with the game and new hacks are a great way to experience what other players love about FFVI. I would also like to see an expanded knowledge base for FFIV and FFV, even though I don't have much practical interest in those games. With your skills you could really benefit community with these, and these could also make you more effective at hacking FFVI as well since they use different mechanics and abilities, but the same baseline concepts. And finally, I think a FFVI advance editor would definitely be a big hit with a lot of people.

Things like making a FFVI port in C# is a good idea in theory, but in the end will only marginally benefit anybody, including you. The port will be useful practice only and the project won't have any staying power once complete. You will have the experience and maybe a little more knowledge of C#, but very few people will play it beyond testing, including yourself, whereas something like a personal FFVI hack project would have lasting appeal because of its originality. A similar case could be made for the SDK project; unless the project is purely for yourself, your hack will get more exposure in the mainstream hack community as an ips rather than trying to propagate it through SDK. Plus a ROM hack allows other members of the community to dive into your code and learn from you moreso than the SDK project would. However, if you are starting to get a little burnt-out on Hex, then a C# or SDK project might be a refreshing change for a little while.

In the end, this is your call, I hope I've at least given you a little bit to think about.