FAir has a bit of start-up compared to his other aerials, but it seems like you're starting it too close to your opponent. Ike's aerial speed (not aerial maneuverability) is pretty good, so try short-hop FAir'ing at your opponent and aiming for the tip instead. If you're up close, retreating NAir is a generally a better and safer option.
With regards to Ike's profits from throws, they're very good but heavily dependent on DI and %. For floaties, try playing around with BThrow, FThrow, and QD; you can usually link either throw into a QD attack at low %s, QD -> JC grab or dash attack at mid %s, DACUS at mid-high %s (it depends, but it's somewhere around 70%-80% for no DI), and QD -> RAR BAir or QD -> FAir at high %s. DThrow is also very good on floaties starting a mid %s, at which you can either QD -> JC grab if they DI towards your back or BAir if they DI towards your front. At higher %s, floaties can get DACUS'd or QD -> RAR BAir if they try DI'ing towards your back. Last but not least, UThrow is a pretty good combo starter and positioning throw at low %s, either letting you link into (reverse) BAir or start juggles with NAir. On fastfallers, you can chaingrab them at mid%-high%s, and you can also QD -> JC grab if they try DI'ing away. At higher %s, you can end the chaingrab with QD -> RAR BAir or DACUS, but DACUS isn't really worth it unless you get the hilt sweetspot.