I communicate a lot online, especially in chatrooms - often on Stack Exchange chat itself, or Discord, or similar platforms, and have been using these platforms to communicate for years. I'm often sarcastic - I like incorporating sarcasm into my communication, and it doesn't help that I like to at times provide "comic relief" of sorts. I'm used to people assuming that what I'm saying is sarcasm, because a lot of the time, it is.
A good way that I've found to differentiate between when you're being sarcastic and when not is to incorporate a specific writing style for being sarcastic, and a different one for being serious. This happened rather naturally for me, simply as a result of being misunderstood a bit too often - it sort of developed as a defense mechanism.
If I'm being sarcastic, I'll often trail off sentences with an ellipsis at the end, and in general adopt a dry, familiar tone. Emphasis on words like "much better" also helps with replicating normal tones for speaking sarcastically. Throwing in emojis like ";)" are also commonplace. Speaking in absolutes also often gives a sarcastic tone.
Yeah, it would've been much better if they'd have killed her off at the end...
Seriously, it would've been better if they had killed her off at the end - it would've resolved the storyline with this guy, and given some resolution to the character.
When I'm not being sarcastic, my tone gets less dry. I sound more like I mean what I'm saying. Drop the emojis. Drop the ellipsis at the end. Sound more "serious". Flesh out what you're saying. For extra benefit, throw on a "seriously" at the beginning, especially if you're switching from being joking / sarcastic to being serious, or use another similar method ("on a more serious note", "to be serious for a sec", etc).
What you wrote - "I agree. Especially if your anime were going to be filler-ridden anyway" - has several things in it that make it sound like you're being sarcastic.
First off, you wrote "I agree". That immediately sounds sarcastic. (I'm not even sure why, but it does. It for some reason immediately gives me the impress that you're not being serious.) If I were you, I'd've thrown on a "seriously" at the beginning.
Second, you're degrading the thing you're talking about, in a way. "filler-ridden" gives the impression that you're being sarcastic because you're putting it down without explaining what you mean, or giving your reasoning.
If I were in your position, I would have gone for something more like this.
Seriously, I agree. It already has lots of filler in it, which is Toei's specialty, so it would actually be a good idea.
While there's still the possibility of this being misinterpreted as being sarcastic, from my experience this will be much less likely now that you're explaining your reasoning, and leading with something ("seriously") that should explicitly tell them that you're not being sarcastic.
While there's no sureproof way to make sure that you're never taken sarcastically when you're not, in my experience, the best way is to adopt a certain way that you use to communicate in each instance, and avoid using communication methods that are usually seen as sarcastic when you're being serious. This will work best with people who you communicate with often and have learned your style of communication, but I've had success in using my two methods of communication even with people who I am not in regular contact with.
As an aside, cultural and language barriers often play an often underestimated role when it comes to sarcasm and communication on the internet. People who don't speak English as a first language often have a hard time picking up on the subtleties that come into play in English, and people who do speak English as a first language sometimes read stuff into other people's messages that the person who wrote the message didn't mean at all. Other cultural considerations, such as not generally using sarcasm at all, can also have an impact on understanding. It's something to keep in mind. Always be ready to explain yourself, and don't be too quick to jump to conclusions, especially if the other person isn't a native speaker.