in the panel settings of time series visual builder you can override the index pattern. you can even set it to * (to look at all index patterns). the only requirement is that all your index patterns have the same time field (for example @timestamp).
then you can plot metrics on fields from different indexes.
you could also do the same using timelion, without the restriction of same time field:
.es(index=myfirstindex, timefield=timestamp, metric=sum:bytes), .es(index=secondindex, timefield=time, metric=count)