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I'd say yes. Because Long Runners are uncommon, there'd be little point to making a distinct trope of "Early Installment Weirdness, except for Long Runners".
There does have to be some hindsight though. If the 7th installment is released tomorrow with another new and experimental mechanic, it'd be way too early to call weirdness on installments 1 through 6. But yeah, commenting on the 3rd out of 6th of the series seems okay.
Edited by KD
Of course. It's still an earlier installment in an ongoing series. Halo 2, despite not being the first game in the series, introduced dual wielding, an element that hasn't appeared in any games since the 3rd one. So to a player who picks up the games with the 4th or 5th one, that would fall under the trope.
Say a Long Runner game series has a mechanic that was only introduced in the third game of the series, but it behaved much differently in that game than it did in the subsequent fourth, fifth, and sixth installments. Would Tropes Are Flexible allow Early-Installment Weirdness to describe the initial appearance of that mechanic in the third game, even though it's not an "early installment" in the strictest sense of the word?