As interesting and awesome as it sounds, having Supergirl(Melissa) and Superman(Tom) in the Flash/Arrow, it has a high chance to ruin the series in general. CW's Arrow and Flash has laid a fairly decent foundation as a good series, even showing some interesting Easter eggs for DC fans (cameo of Hal Jordan in Arrow and the hint that he was selected to join the Green Lanterns in Flash).
But, as there no mention of Batman (any) nor Superman(Tom)/Supergirl(Melissa) in the Arrow/Flash series, its gonna be a hell of a hassle to introduce them in the same universe.
Saying they've cross over to that universe (CW) via inter-dimensional portals would make fans cringe their teeth, as they will complain about the series is running outta ideas (milking the living hell outta the idea of using of inter-dimensional portals) and it will be very confusing for new audiences that do not know of the old series(Smallville) in the first place.
Seriously, having Jay Garrick in Flash via inter-dimensional portals even though he is actually Flash's senior and have Oliver Queen trained under League of Shadows and Malcom Merlyn as Ra's al Ghul is considered rather bold for CW, but a bit confusing to new DC fans.
But there are a few ideas they can use, of course if they choose to . To introduce Superman, they can try introduce Clark Kent (pre-Superman) as a vegabound wandering in to either Star or Central city and helping Arrow/Flash kicked off as a start to the road for him to be Superman. Supergirl can then be introduced in like years down the road in the series timeline (For us maybe seaon 5 or 6 if it goes that far). Wonder Woman can be spontaneous as the Amazon island was meant to be kept a secret. Batman is gonna be harder to introduce as the League of Shadows is introduced in Arrow and currently lead by Malcom, its gonna be hard without making it awkward. (Imagine Malcom telling anyone "Oh btw there was a person that was suppose to succeed Ra's, I forgot his name but his is known in the League as al watawat, maybe he is the bat-person that appeared in gotham recently). They are going to introduce Hawkgirl so thats done. Martian Manhunter can be spontaneous as well (Alien crash lands in the current timeline)
Bottom line, if they really going to have Tom Welling's Superman or Supergirl to appear in the current Arrow/Flash series, they have to come up something better than just inter-dimensional portals.