- A lot of potential headscratchers (like how Toyman and Prankster knew that Pete Ross knew Superman was Clark Kent) are going to be answered by the fact that Mr. Mxyxsptlk was secretly munipulating events until the end.
- Why did Jimmy use the Elastic Lad serum when the pool that gives you Superman's powers was right there being used by Lana? Wouldn't two supermen be more useful?
- Nostalgia (both on the author and on the character's part), perhaps. Or perhaps because the Elastic Lad powerset was more familiar to Jimmy than the Kryptonian superpowers, thus requiring less of an adjustment period. That's about all I can think of, off the top of my head.
- In addition, you want a variety of powers, because you can see how easily Lana's powers were removed. Jimmy as Elastic Lad did disable the device.
- In a meta-sense, probably because Jimmy's Elastic Lad persona was well-established in the pre-crisis comics and the whole story was a loving homage and farewell to that era, so it made sense for Jimmy's final appearances as this version of the character to involve one last hurrah as Elastic Lad.
- Was Superman planning on setting up another Secret ID after he was exposed as Clark Kent? There's no indication of this, even though he's clearly smart enough to do so, and he has the resources of Batman and the JLA on hand. It'd probably be psychologically straining (especially if he figured he could never get too close to his friends again, because they'd be ready for it this time), but it beats being Superman 24/7, which he's repeatedly admitted would drive him insane.
- Considering that it becomes almost immediately apparent to Superman that all of his enemies are teaming up to curb-stomp him in a final battle royale, it's probably less that he doesn't plan on doing so and more that he simply both doesn't have the time and sees no reason in immediately doing so if he might be killed for real within a matter of days. Under different circumstances, he could well have done so or already had done so (at least provisionally) — after all, Jordan Elliot had to come from somewhere.
- What killed Supergirl in this timeline if Crisis never happened? From a meta standpoint, it might've been cruel to kill her again, but frustrating to her fans to show her finally replacing her cousin as earth's guardian when they doubted they would see her again, but the rest of the story never pulls punches, and has Superwoman survive, despite also being retconned out of existence by Crisis.
- The same thing. For some number of months after the end of "Crisis" (but before the actual "Man of Steel" Byrne reboot miniseries), the pre-Crisis continuity continued to exist for Superman, despite his now living on a now-unified, single Earth. (The reason why Captain Marvel appeared with the other heroes at the end of "Man of Tomorrow?".) Thus, Supergirl was dead due to the events of "Crisis"; Superman still recalls that, plus his pre-Crisis career/life events, as did the general public. Once "Man of Steel" came out, the post-Crisis continuity became firmly established for Superman.
Headscratchers / Whatever Happened to the Man of Tomorrow?