Since Vixen 2.1 has a limitation of 1000 channels, I use Vixen+ for sequencing. It can read/write files in versions 2.1 and 2.5, and has it's own Vixen+ format. But it can also save the files directly in FSEQ format.
Vixen+ doesn't have the 1000 channel limitation and has better grouping capabilities than either 2.1 or 2.5. However, Vixen+ does not have a player or scheduler. Development on the product stopped about 2 or 3 years ago.
Currently, my sequence profiles are set to 999 channels so I can save them as version 2.1 and use the tried-and-tested Vixen 2.1 to schedule and play them. If I decide to go past 999 I'll save them as FSEQ files and play them with the XLights scheduler (or a Raspberry Pi).
When it comes to sequencing, I fully admit that I am a curmudgeon. I prefer to use the grid approach to sequencing where I have direct access to each cell instance for every channel over the object-oriented method of defining the properties of a prop and then dropping the prop into the sequence over a period of time. I look at it this way: the light can be either on or off. I already know what color it's going to be because the channels are set that way in the profile. Each of my props has its own channel start address so they're easy to use. I'm not a pixel guy -- I like discrete, individual channels where a channel may be a string of 25, 50 or 100 (or more) lights, or perhaps just a single bulb. I've tried defining a few props using the newer sequencers but I don't see the benefit over what I'm currently doing because none of my props need 2 or 3 universes of channels: they need 4, or 8, or sometimes just one or two channels. So in my pea-sized brain, going to the trouble of defining multiple properties of a prop when it has only one or two channels to begin with is just extra, time-consuming work when all I want to do is turn on one or two channels.
That said, I have great admiration for the teams that have developed these advanced sequencing tools. They are space-agey, powerful sequencers, to be sure. They're just not my style.