Ever think people just gotten sick of MHA and Haikyuu!! starting in August 2017? Problem solved. No, seriously, you said yourselves that MHA just getting a lot better again, meaning around August 2017, the story must be quite crap yeah? (If you said it is getting a lot better now then you're applying that the series quality went downhill for some times). Quality decrease > People don't enjoy it > no votes > went down in ToC placement. But yeah, let's blame it all on EiC beause why not.
*EiC did decided which series in which position in ToC but if series have significantly lower votes, I don't think he will put that series in higher placement than any series with higher votes than it (except for OP obv).