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RE: Towards a reputation system suitable for SteemSTEM
If the point of the reputation score is only to decide how to vote on the latest post, then it does make sense to privilege the recent stuff. I think I was thinking it more like an overall badge of merit (basically, a replacement of the steem rep number, since you're making an independent website) and felt awkwardly about discounting the historical contribution of valuable members who for one reason or another are not as present, currently, on the platform.
For the moment, the score is just something funny. Like you said, a kind of badge of merit. This is by no means affecting any future vote as the rules for votes are independent (and clearly stated).
The decaying reputation is more to have a way to slowly remove users that have left. There is a difference between not being present and having left, which is why the half-life is large. However, this may be improved (cf. the above comment by @tarazkp).