Some prefer the security and reliability of their own desktop (which definitely requires you backup regularly and reliably and store off-site). If their only accounts are for a private trust or other small activity, they may appreciate the cost savings of a cut-down version of the product - only recently available in Reckon One in the cloud.
Advocates of cloud-based systems argue that in fact, their systems are more reliable because they have dedicated backups and extensive security. Plus their users are always on the latest version of the software with no need to upgrade. Note that the two traditonal desktop products (MYOB and Reckon/Quickbooks) are still available on the desktop, but you pay an annual fee, which sadly seems to rise as exorbitantly as cloud software, despite being well developed. Others prefer to be totally in the cloud - accessible from anywhere. Many organisations are spread out and really benefit from this. Still, others just want a fast reliable system - and could benefit from their accountant using the same online system. While the early days of "the cloud" involved a significant sacrifice of performance, that is less so today.
So there are many factors here. While a desktop system is faster and may be more reliable (if it is backed up regularly and reliably it's not dependent on access to the internet and less prone to hackers, etc), the convenience of access from any system and the reliability of backup and the widespread use of the internet mean more and more people prefer their accounting software to run over the internet. Unless there are major hiccoughs with the internet (e.g. nuclear war, solar interference, or your favourite doomsday event), then this trend is going to continue - but we're not sure if it will ever be the only choice.
One obvious advantage of cloud systems is how cheap they are, right? Well, in his article "The host with the most" by Glenn Baker in the September 2014 copy of NZ Business, he says Grant Cowie (CEO of desktop system MoneyWorks) points out that it's difficult to see how paying a monthly fee in perpetuity is more cost effective than a one-off purchase. Of course, there's a lot more to this issue than just upfront fees - there are upgrades, backups (often totally ignored with cloud-based systems until you want to change), and many other factors.
According to some of the marketing hype, cloud systems avoid the need for accountants. We went through much the same turmoil when MYOB and QuickBooks became popular. I believe the same applies to software in the cloud. I did wonder if Xero might have cracked it - but their developers are no match for "smart" users who can find all sorts of not so smart ways to beat the system. And as they add new functionality, for every hole they close others are created. Basically, if you have no accounting background, you should get your system checked by someone who has some proven accounting expertise.
Despite the hype, there's still no common, one size fits all, answer for everyone. Each person has to identify what's important to them, both now and in the foreseeable future. The most important advice we give is not to rush into whatever choice you are faced with until you have a good understanding of the features, and have looked at the alternatives.