You didn't say a clone you said Sephy. Despite no clones actually physically looking like Sephiroth, or anyone but Sephiroth and Jenova being able to wield that sword, these aren't the most obvious flaws in this theory. The most obvious being, WHY BOTHER? Jenova had a perfectly good puppet inside the building. A Sephy clone is nearly as unrealistic as Sephy himself, given the only one with any real strength still need several people with him to get into the building, and he still managed to get caught.
The tattoo would be explained if it was Jenova, Sephiroth was experimented on more than anyone by Hojo, he would probably have a tattoo.
Cloud was asleep, and not in control of his mind at the time. Very much like Mideel if you want to make the comparison. Even if he had been awake, Jenova wouldn't want him to remember, it would have given too much away at the wrong time.