Like anything else, the answer is ... it depends.
1. As far as CLCs go, there is no CLC that has better performance / noise than comparably priced air coolers. So when under $150, the air cooler is not only leak worry free it's the better option from all angles. The only advantage of a CLC that I can see is you don't like the look of a big metal heat sink but looking at a big radiator is OK.
If you keep a CLC long enough, the corrosion inhibitors will use up their useful life in 18 - 24 months and after that galvanic corrosion will accelerate, much more so than in other water cooled systems because CLCs use a cheap, thermally inefficient aluminum radiator. Having different aka "mixed metals" in a water loop is a very bad thing and the corrosion can not only lead to leakage but ....
https://martinsliquidlab.wordpress.com/2012/01/24/corrosion-explored/
The performance is also gimped by the weak pumps and extreme speed fans needed to offset the low thermal transfer of aluminum.
2. Custom loops are, as you likely expect, designed around performance and noise rather than trying to get the price low enough to compete with air coolers. You can buy 'kits' for a reasonable cost or go all out with custom designs where the water cooling components for a particular aesthetic along cost upwards of $2k. Possibility for leakage is very small and 99.8% dependent on user assembly. "Dry Run" testing should always be performed with only the pump powered and all PC components off.
3. The intermediate ground is OLCs or Open Loop AIOs like the Swiftech, EK and Alphacool units. As expected the EK units, I would say are the highest quality and they are very easy to add extra components. It must be noted that there was a flaw in the original units:
a) For EK, the first units off the line had a faulty O-Ring and a small % of units leaked over time. EK revised the design and released version 1.1 which doesn't have this issue. They are now moving to a modular approach where you buy a radiator / Pump assembly, CPU water block assembly and, if desired, a GPU block assembly (installed on GFX card). Each part "snaps together" and you never have to add a drop of liquid yourself ... availability if 4th quarter.
https://www.ekwb.com/news/ek-is-announcing-modular-liquid-cooling-products/
https://www.vortez.net/news_story/ek_water_blocks_teases_ek_mlc_modular_liquid_cooling_solutions.html
Jump into this thread for the non-modular designs
http://www.overclock.net/t/1566468/ek-predator-club-discussion-thread/6120
https://www.youtube.com/watch?v=Sq4iNbCD844
b) Swiftech was the 1st to enter this category, has a built in reservoir to view coolant and is much less expensive. They crush any CLC on the market and are less expensive than many CLCs (Kraken X62) ... they are louder than the betetr air coolers but 12 times louder like the H100i. We have done many builds w/ the Swiftech units.
https://www.youtube.com/watch?v=PYKdKVxbnp8&t=1379s
http://www.swiftech.com/aio.aspx
The initial Swiftech designs also had a design flaw if ya could call it that in that they had a bleed screw in the acrylic reservoir. If over tightened by the user, you could crack the acrylic which could cause leakage. The bleed screw has since been removed... (about 2.5 years ago).
As far as the upgrade goes, unless you are overclocking, there is no reason to use anything other than a stock cooler.