the real reason

Mukuro's real plan in the first season was not to kill Tsuna, but be able to take over his body. Mukuro had high hopes for his grand, master plan to engulf the world in darkness and cause something of a world war between nations. He wanted to eradicate humans entirely because humanity, to Mukuro, is a disgusting thing. For all that humanity had put him through, it's no surprise that this cynical attitude rests with Mukuro for the rest of his life.

It's straightforward with how this works -- Mukuro isn't a bad guy just to be bad, after all. He was orphaned at a young age, taken into a family of mafioso and by the looks of how his childhood goes, once he was adopted it seemed like the Estraneo family started getting slaughtered, give or take 1-2 years. The slaughter is not what made this boy bitter, but the expermintation of young children and himself (also a child) by their own family, the Estraneo. Dangerous experimentation to produce weapons to fight off other mafia. The lives of the Estraneo children meant nothing if they could not be a successful tool to fight; and that alone caused their downfall.

By this time, Mukuro had been able to start controlling his half-brother, Lancia. In order not to not to get caught, he'd used Lancia to commence killing off whatever was left of the Estraneo family, and not before long, all of them were arrested and thrown into Vendicare prison.

To Mukuro, taking down the underground mafia was one of his strong ambitions. The very existance of the mafia sickens him, so therefore, by taking control of the heir to the strongest family of the system (Vongola 10th), he could start his plan to "purify the world" and move to influencial leaders of the world, with the use of the Possession Bullet. Think of it as a world war. Killing Tsuna wouldn't help him in any way, and besides, with the power of possession, the six paths abilities, and illusion -- there's no way he'd do something so powerful without the use of another person. And besides, let's remember that Mukuro sees humans as no more than 'toys'.

I think that Mukuro had good intentions for the world despite the fact he wanted to engulf it in darkness. From the way he was treated as a child, all he'd ever witnessed was the cruelty of humanity and only found revenge within his cause. I'm not saying that his intentions were the best and should have followed suit and that the world deserves being engulfed by darkness and humanity gone forever - I'm just saying that in a twisted way, he wanted to do something about wickedness in the human's world.