While I agree factions should matter, I wouldn't have come to the conclusion of your ideas. Interesting enough, I would quite like to try them, it might emphasize differences and really have an influence on how factions are viewed. Maybe not make the symp loss severe, I think one pooint would be enough (if the thing is tried at all) to bring the point across. Could make things interesting.

On the thread title, what could make factions matter more:
-) Having the vote for representatives be carried out
-) Having faction representatives have some possibilities for their faction (e.g. setting prices of FSM Items in certain ranges, being able to set guards twice a voting period (for example switch between copbot behaviour and faction behaviour or give money for additional placements in the HQ), set a flag if runners are punished for trading FSM items to the enemy (regarding thread openers ideas), ...
-) Have more faction guards / faction members in the open world that react to enemies. At the moment there are only Storm Bots, TG listening posts and HQs I think(Canyon Military Base and Tech Haven ARE HQs in my opinion, btw we lack more Turrets in TH )
-) Have PvP Missions in the citycom against enemy factions (e.g. Kill 5 Fallen Angels for Tangent Technology runners)

I am sure there could be more