Heracles was a son of Zeus, and Theseus was just a regular Joe. Heracles was half divine, that definitely gave him an edge of Theseus in terms of being praise-worthy, but this shows that Theseus is more like "one of us", just an ordinary ancient Greek I mean. Also, heroes in this time period all went through wild-ass challenges. It simply proved their merit and showed that they could kick ass for your town or country or tent. Being that Theseus was not part god, it makes his missions seem more impossible.
This brings me to the opposition of the heroes. Heracles had it bad because Hera, Zeus' bitter wife, hated him because Zeus cheated on her to create the guy. So, she sent snakes on him when he was only 2 years old. He of course ripped the snakes into pieces, but that's because he's Heracles, you can expect him to do things like that, even if he is a baby. Theseus however had a king for a dad named Aegeus, cool yes, but his dad slept with Theseus' mom on the side, and 17 years earlier, before heading back to his kingdom, Aegeus told the lady "hey hoe, if it turns out to be a son, tell him to take my sword and these sandals and come find me when he's of age".
So once coming of age, Theseus finds the sword and sandals and journeys to Athens to find his dad. Well let me tell you about his trip. Because you want to know. Anyway, Theseus' stories are primarily involved with some brute who is beating the tar out of travelers, and then Theseus comes along and gives them a taste of their own medicine. The stories are very entertaining and funny, mostly because these guys' methods of hurting people are for the lack of a better word abnormal. Like for example the robber Sinis, who grabbed people on the roads and bound them between pine trees that had been tied the ground, and after fastening his victims, he let the trees go, tearing the unlucky fellow from limb to limb. So Sinis snuffed it. Apart.
Meanwhile, Heracles' labors weren't even usually against people, he was always fighting beasts and monsters. He's the number 1 beast-tamer of Hellenistic world I tells ya. Theseus' deeds are more noble I think because he beat up bad people, not a few animals. The dude got something worthwhile accomplished! He cleaned up the roads! Heracles is again, f'n Heracles; his missions are supposed to be hard, but everyone reading the stories knowing he's going to win in the end. No one knows if Theseus is going to make it.
As for love interests and helpers/sidekicks, both have interesting stories that I won't really get into, save that Heracles is a bit of a manwhore and liked to get around. I don't think parents would want their kids growing up to be a guy like that, whether it's today or 2500 years ago. But back to the point, Heracles had 3 official wives, 1 he murders, 1 murders him, and the other he meets through a friend in the afterlife on Mt Olympus. And as for helpers, he's Hercules so he doesn't need any, though he does have a homosexual relationship with a little dude who followed him around for a few adventures. I'm not judging.
Theseus' helper/lover was this great gal named Ariadne, and she is involved in the famous story with the Minotaur and Labyrinth. You should read it, not to mention you will realize the story is replayed or parodied everywhere today.
Eventually however, Theseus dies. Nothing special, he just dies. I think this is perfect, he's the epitome of what a young, ambitious, ancient Greek guy would want to be, as Theseus' life doesn't seem that improbable and yet he's famous.

With the purpose of a hero inspiring people and fulfilling people's desires for entertainment, hope, ambition, etc., Theseus wins over Heracles in my mind. We imagine ourselves even today as famous persons, whether current or past. They may not be all perfect, but neither were these Hellenistic heroes. But we can't deny that we haven't wished at some point to do things like star in this movie, play this professional sport, lead this country, win that battle, write this book, etc. We can identify with Theseus better, and I think YOU should read up on his stories and put Heracles on the back-burner.