Mid 2006 to last quarter 2012, it's the same car. No difference at all apart from very minute unnoticeable changes in the interior mainly such as silver accented steering garnish 2009 onwards, different fabric 2009 onwards in Oriel, 2010 onwards in hardtop, CD changer built in panel (Oriel only) starting 2008 mid, an upgraded power window switch, upgraded power steering pipe and upgraded timing adjuster along with bigger belt.
Overall it's the same car, however the 2012 onwards 9th Gen Civic is a totally different story.
About the Prosmatec transmission, since 2004 onwards i have always kept an automatic car which is a must in the hectic rushy traffic of lahore. Also once you are constantly cruising at a speed of 120 plus on the motorway, gears don't matter. The Prosmatec isn't exactly boring as well. With a 140hp even the automatic isn't as boring to drive. Though I do admit sometimes manual is missed, but for a habitual auto driver that happens only sometimes. Don't exactly feel I miss out much.
Manual Civics kept getting extinct with every passing year with the result that manual transmission is now completely dead in the Civic name with the 10th Generation Civic.