Bike Upgrades

I think upgrades are important, and I think it's necessary to spend money on necessary upgrades over fancy accessories, provided they don't affect the feel of your riding experience.

Your only option to reduce the cabling would be a wireless electronic groupset, and these do not come cheap.  Sram Force is the entry level I think.

As others say, some nice wheels are good to have, and combined with decent tyres will make a difference to the ride.  

I also recommend upgraded handlebars.... don't cost a fortune, and as a key contact point will change the feel of the bike (Prime Primavera aero bars are great... deal on at the moment, though this is via Wiggle!).  Consider getting some narrower ones to suit you.  They may also improve the cable routing. 

If you do change the crankset to something by Praxis (although I'd have thought that upgrading the wheels first and foremost) whatever you do use another manufaturer's bearings. Praxis must make their's from cheese, I've been replacing mine annualy these past few years. With my very, very, modest power output and rather average annual milage that's really poor. 

Some good advice was given !
Conti gp5000 28mm tyres , are a good investment. Then wheels.
A simple solution for cable spagetti is cheap cable wrap fron diy store.
I use it on all my bikes to make 4 cabeles into 2 . To make the cockpit look more tidy
Ride safe !

Looks to be a non-series crankset, so I understand your wish to upgrade but get your money's worth from it first. 

Agree that a "best" wheel set and tyres might be more worthwhile - e.g. DCR, Hunt or even try building your own. 

Endurance bike with 50x11 topmost gear - if you were road riding and pushing that gear, you'd probably be going too fast. Maybe one of the Miche cassettes that start at 13t when you make your drive train change? 

I think most seasoned riders would not start with cranks.  Simple things can make a huge difference first: quality tyres, good brake pads, season appropriate clothing and a bloody good pair of shorts would be top of my start list.

Seems to be a pressfit bottom bracket which is a bit trickier to deal with at home, as Richbeck suggests you will get more benefit from new wheels, don't forget to add the cost for some top quality tyres and latex tubes.

Cranks are a simple home fit although you will need a few specialist tools - Need to check BB and crankset compatibility.

I'd leave the cranks and get some new wheels - Handbuilt all the way for me from DCR wheels!