For starters:
1) clean the hell out of that overflow bottle, or get a new one
2) move the power steering reservoir and clean it up
3) aim for all your hoses and piping to be one colour. I suggest flat black. Get some liquid gel tyre shine, and attack your black hoses. (radiator, fuel, etc)
4) take that fuse box lid off the battery and put it back on
5) if you want to paint something in there black (like the manifold), then make everything the same shade of black. matt black sanded really well, works MUCH better than gloss black. Paint the supercharger, repaint the manifold, your engine crane hoist point, and if you can, take apart the alternator and paint that carefully.
6) try and make your hoses follow the lines of the engine, and emphasise them. eg: your plumb-back hose. Perhaps have it follow the line of the rad hose to the front of the car, then turn at a right angle (get a neck for it) and run across the front of the car to the airbox. Straight lines look neat.
7) line things up. Your BOV, get that in line with something. Pressure gauge and t-pipe vac hoses, get them lined up and cable tied to things. That wiring at the back of the engine bay? Tuck it back up into its factory clasps.
8) remove that goddamn "danger" sticker from the fan shroud.
9) where possible, cover your coloured wires with large black ribbed covers, and combine it with factory wires
10) make sure those silicone hose bends are black next time I see them
11) your metal aircon hose adapter running into the firewall. That needs to be black.
12) get that factory air baffle back infront of the fan shroud, you can see the radiator core from the top and that's ugly.
13) hope for the best, V6 engine bays are UGLY!