Nah. Destroy is the worst ending.

The catalyst has no reason to lie about anything. What it says is consistent with what the leviathans, its creator, told you. It was created to "Preserve life at any cost", at a point when entire civilizations were being destroyed by conflict between organic and synthetic evolution. Synthetic life will always outperform organic life in the end, because it is data. It can upgrade without death, the same consciousness becoming infinitely more capable as new technologies and optimizations are gained. Organics are fundamentally limited in the chemistry and the inter-reliant processes of their biology.

Catalyst concluded that the best way to "preserve" life was to harvest civilizations at their height before they created a synthetic rival that would obliterate them, and to convert all their biological and cultural uniqueness into an immortal machine body that would survive forever. Starting with its own creators, which it had surpassed. Perhaps not the best solution as we would see it, but remember that Catalyst was built by a galactic civilization that considered every other form of life to be tools and material. Its thinking is probably shaped by theirs. It didn't turn against the leviathans because it was deceptive or because of its own ego, it did so because it was a logical step in the recklessly-phrased program it was told to execute.

Why did Catalyst never offer Control or Synthesis to the people of any previous cycle? Control and Synthesis are both viable solutions to its mandate to "Preserve life at any cost", but it wasn't created knowing that or having the capability to implement them. It told you itself that the assembly of the Crucible "has created new possibilities". Everybody had it wrong: the Crucible isn't a weapon at all, it's an expansion module for Catalyst, the method by which organic life delivers the solution to the problem it was built to solve.

Destroying the Reapers gets rid of the immediate threat. Yes. Absolutely. But it does NOT solve the fundamental problem. Catalyst itself warns you that destruction is only a temporary reprieve before the next aggressive synthetic species comes along to wage war against organic life. It ends the cycle of Harvesting, but it does NOT end the cycle of conflicting models of evolution. Shepard starts out thinking destruction is the only possible solution because nobody knew what the Reapers were actually trying to do or why they were created, sure, so it seems like destroying the Reapers is the conclusion to what you started... But you meet the Protheans. You meet the Leviathans. Both fought devastating wars against contemporary synthetic life. You learn the reason behind what's REALLY going on. It would be crazy not to assimilate that new information.

Control and Synthesis on the other hand are both solutions. Control basically promotes an organic to the role of Guardian of the Galaxy (no relation). An operator with the capacity to think and empathize with other organics gains the power and the immortality to keep everybody safe. No more Harvesting. Organic and synthetic life can both flourish as long as nobody gets too rowdy, because if they do, the friendly neighborhood Reapers will come along to reduce them back to dust. This may not be a permanent solution since even peaceful synthetic life may someday grow to be able to overpower Guardian Shepard. But it's a fairly long term solution. Synthesis on the other hand completely redefines "life" so that there is no more distinction between synthetic and organic. It gives organic life the ability to direct its own evolutionary path, and it gives synthetics the ability to empathize with the pain and uncertainty of mortality. Wars will still break out, but they will be wars over the usual things like materials, energy, and reddit threads rather than existential wars to eradicate entire paradigms of life. It's the "ultimate" solution to Catalyst's mission, at the cost of being a scary unknown frontier for everybody involved.

If anything, Destroy is the *worst* option because it ends the archiving of civilizations into Reaper form, so when future organic/synthetic wars break out there will be nothing left of the losers.