Who was the leader of the Senate?

[Icelerate]

This might be odd but I forgot this detail. I'm pretty sure it is supposed to Sephiran and Lekain is the second in command but Lekain ended up influencing the other senators giving him more power over the Senate compared to Sephiran. 

So Sephiran is the de jure head of the Senate but Lekain is the one who is the de facto leader of the Senate. 

[Interdimensional Observer]

You've pretty much answered your own question. And as a reminder, Lekain says this:

Spoiler

Lekain:
“The year was 640, Begnion era… The empire had been without an apostle for 15 long years. The senators were being constantly harassed with complaints from the people. There had been nothing like it in history. The voices calling for young Sanaki to be crowned grew louder every day… You had just turned five years old when the senate welcomed you to the throne as the new apostle. Ah, but my young mistress Sanaki, what a difficult child you were. After being separated from your mother, you threw tantrums, you screamed and cried constantly. Your conduct was hardly befitting an empress of Begnion! Everyone was at a loss… You wouldn’t even stop mewling and crying during official proceedings. But then along came our youngest senator ever, Sephiran, Duke of Persis. When he took you in his arms, you immediately stopped crying. You even smiled. We had to take advantage of this obvious miracle. In an unprecedented move by the senators, we elevated Sephiran to prime minister, keeping him serving as close to you as possible. This plan, radical as it was, proved far more effective than we dared dream. A young, handsome prime minister and an adorable moppet of an apostle brought the people’s support to incredible new heights. Apparently the common citizenry is gullible enough to blindly follow any leader who is sufficiently attractive. Enamored as they were, no one ever seemed to care whether or not you could hear the voice of the goddess. With the new apostle and prime minister, the political landscape became unrecognizable. Even in the face of overtly unreasonable legislation, the two of you would stand on the balcony… A smile and a wave later, the people would cheer and go on with their happy lives.”

Sanaki:
“…”

Lekain:
“It was too good to be true, however. Both of you were only meant to be puppets! Each year you interfered with our government more and more, imposing your soft-hearted ideals over our sovereign rights. Were such trivialities as laguz slavery and sending troops to Crimea worth making issues of? The pair of you were becoming an increasingly bothersome thorn in our side. And then this war against the laguz forces… You went so far as to expose our previous indiscretions and demand reparations for the sub-humans. This was unforgivable. Clearly you both had to be removed. Sephiran would be falsely accused and jailed, necessitating his removal from office. The apostle would suffer a sudden illness, and be excused from official proceedings. Or so we intended…”

Sephiran was supposed to be a puppet for the public. In practice, even if he did not stop Lekain, he was apparently threatening his position.

Of course, Sephiran would likely not actually get rid of Lekain, having a corrupt leader who could bring in the necessary Chaos was in a way expedient. Although you could argue beheading Lekain and directing foreign policy directly would have been better.

[smgrinus]

The lore isn't too clear on who was the head of the Senate. Sephiran is mentioned as its most senior member, while Lekain is touted as a high ranking member of the Senate in some of the corrupt circles. It is never clearly stated who is the highest far as I can tell. Lekain does seem to have a lot more influence over the other senators and dukes then Sephiran although that might be purposeful on Sephiran's part. 

[Zihark11]

Sephiran technically has the higher position then Lekain but as Sephiran has given up on the world after such long torment, gives Lekain no leash thus he does whatever he wants.