One of the most evident traits of Tom Sawyer include his inability to finish what he starts, his exagerated plans and plots, and his lack of everything to put any of this in place.
When you asked the question, the first thing that came to my head as an avid fanatic of both Huck and Tom was "Tom???!" precisely because when I teach the novel I always divide my students between the Hucks and the Toms, often specifying that Tom is the typical daydreaming, fantasy-making, and self glorified "man with the plan". Yet, in thhe end, like the previous postings stated Hucks always end up fending for himself, doing things that are no-nonsense, and ending up getting the job somehow done and finished.
Huck's wishing for Tom to help him escape is ironic because when Tom is around to help Jim "escape" at the novel's end, he unnecessarily prolongs Jim's captivity to implement his Romantic plotline. When Huck is trying to escape from Pap at the beginning of the novel, he longs for Tom's "fancy touches" for his escape, but Huck escapes flawlessly and practically from Pap because of his pragmatic intellect.
If Tom had been there, he most likely would have asked Huck to allow him some time to come up with his escape plan and then would have developed an elaborate story to accompany his plan, which would have made it ineffective and would have put Huck in even more danger from Pap.
Twain characterizes the two boys in this manner because Huck is Twain's voice--the voice of the Realist, someone who is practical and usually logical in his thinking. In contrast, Tom represents the Romantics for whom Twain held so much contempt. He believed that Romantic authors drew out their writing unnecessarily by adding unrealistic elements and too many flowery descriptions. Philosophically, any plan that Tom develops cannot be successful because Twain would be admitting that the Romantics trump him and his own philosophy of writing.
This is only ironic when you think about what happens when Tom is around to plan an escape. Specifically, think about how Tom goes about planning for Jim to escape when he is captured and held at the Phelpses' home.
Tom insists on making a hugely elaborate plan that is based on his memory of what happens in novels. It's a totally pointless plan that makes Jim do all sorts of unnecessary things. So it's really not all that helpful to have Tom around when planning an escape.
The irony, then, is that Huck is wishing for something that would likely not have been helpful.