The Ion Blaster is an all-around good weapon to have, IMO. The Fusion Cannon is a heavy hitter and has some nice splash damage. I personally also like the Magma Frag Launcher, especially in close quarters
Warcry is a necessity for a Leader. It boosts not only your abilities but also your teammates', and in games like Power Struggle or Conquest where everyone is congregating in 1-3 key areas, it's a good ability to have. Don't have any other suggestions for your other ability, that's personal preference.
For upgrades, definitely think about getting Martyrdom, which drops a Thermo Mine when you're killed (like MW2). The upgrades that increase the range of the Thermo Mine and the radius of Warcry are good, too. One upgrade I haven't tried yet since I'm not a high enough level but I want is the Reserve Power Cells (which is basically like Final Stand/Last Stand in MW2). It allows you to linger around for a while and keep shooting even after your energon levels have dropped to zero.
I've got two Leaders right now. One of them is armed with an Ion Blaster and Magma Frag Launcher, uses Warcry and Barrier, and has the Martyrdom upgrade and the upgrades that increase the range of the Thermo Mine and Warcry (I think). Pretty standard. My other Leader I've outfitted for heavy hitting and offense: Fusion Cannon and Magma Frag Launcher, Warcry and Moleculon Bomb, and...I don't remember what upgrades I gave him at this moment