The shuttle may make for a better alternative in some situations but I think you guys are being overly harsh regarding the public buses. Let's look at it point by point.
PURCHASING TICKETS: You may be well advised to purchase bus tickets a day ahead during weekends during the dry season, but during the week and during the wet season it may not be necessary. Even if it is that does not necessarily mean an extra trip to the bus station the day before. One could simply ask someone at the front desk of their hotel if they could get someone to pickup tickets for them and I'd be willing to bet most hotels would be willing to help out with this service. Tipping the guy a couple of bucks for his trouble will still come out way cheaper than paying $20 each way for the shuttle. And I can't see how its could be counted as a major disadvantage of taking the bus if you have to reserve a day ahead for the shuttle as well.
BUS STATION LOCATION: Yes, El C, the Coca Cola Terminal can get a little rough and that's why I'd definitely avoid arriving back there after dark. However, the buses to Jaco take off during the day and that area is not much worse at that time of day than many other nearby areas we already routinely visit in the Zona Rosa (e.g. the Calle 6 Pensiones, MP 747, etc.) and significantly better than the Mercado Central which many of our members also like to visit. I'd also be as wary as you if I couldn't see what was going on around me, but fortunately I don't have that problem. Obviously, as in anywhere you go in SJ, but particularly here, you pay attention to your surroundings and don't do anything stupid like walk around with your daypack hanging open behind you or nodding off on a terminal bench. Daytime crimes are much more likely to be of the stealth/theft variety than outright robbery/muggings. One just needs to stay on their toes.
BAGGAGE THEFT: If I'm going for just a night or two I can usually stuff everything I need in a daypack which I can keep with me always. If it won't all fit, I pack just my clothes and other non-valuable items in the bag that goes in the luggage compartment and carry my camera(s), passport, money etc. in my day pack (and a light jacket or sweatshirt in case it gets chilly, but that hasn't been a problem on the buses I've been on). BTW, it also doesn't hurt to use a bag that is not too fancy if not even a little beat up rather than something that marks it as belonging to a rich tourist. I usually wait until they open the lower compartment and start loading bags and wait until I see mine is well buried before I get on the bus, particularly if I have someone else with me that can grab and hold a good set of seats for us. The front end right hand side affords the best views, most comfortable ride, allows me to watch if anything happens with the luggage compartment at intermediate stops and allows me to get off quickly at the end to watch the unloading of bags. As far as my daypack, that would NEVER go in the overhead bin. That is an open invitation for someone to mess around with it on the pretense of getting something out of their own bag when you're not paying much attention. I also never place it under my seat which allows the person behind me to get to it with out my noticing. These are well documented risks and anyone who has been ripped off in this fashion either hasn't done their reading or simply slipped up. I always carry my daypack on my lap or wedged between my feet and zipped up (I even have a little travel padlock I use). If I decide to take a nap, I hug the bag to my chest with my arms securely around it (or use it as a pillow). However on a short trip to Jaco, I wouldn't need or even want to sleep. The ride is scenic and only 2.5hours long. And despite all these precautions, I've always felt perfectly comfortable on buses and at ease and most if not all the people near you on most routes will be regular ticos just trying to get somewhere like you, not crooks looking to rip you off. In other words you just need to take sensible precautions, but you don't need to be paranoid.
BUS STOPS: There are 2 types of bus routes, direct and indirect. One would probably never take the indirect with its frequent stops (e.g. the direct to MA is 3.5 hours the indirect takes 5). The direct buses usually make a few intermediate stops too, but not many. Usually what few stops there are of the quick hop-on or off the bus variety with no messing around with the luggage compartment until the final destination. The 2.5 hours bus ride to Jaco does not really allow for many stops if any since that time span is not much longer than it would take to drive straight through to Jaco by private car. The last bus I took to Monteverde made exactly 1 stop - a scheduled pit stop. And the bus from Arenal made 5 minute stops at the San Carlos and Alajuela terminals and maybe 2-3 elsewhere en route to allow someone to hop off.
SCHEDULING: Ultimately, IMHO, whether to take a shuttle or a bus comes down as much to scheduling as it does to price or security. The Interbus
http://www.interbusonline.com leaves for Jaco at 8:15AM. Grayline
http://www.graylinecostarica.com is another shuttle service that is usually a little cheaper than Interbus but to Jaco the cost a couple of bucks more and leave at 8AM. Either of those times would work fine for me and would get me to Jaco nice and early to get some quality beach time. If I were dragging from a late night before or if I was counting on a chica companion to show up on time (yeah right!), it might be a little more problematic. Unfortunately the next shuttle van doesn't leave until 2 or 2:30 in the afternoon meaning a late afternoon arrival in Jaco and barely any beach time. OTOH, it would allow me to slip in one extra Oasis or ZB massage session before I headed out. The public buses run a little more frequently allowing more options in addition to 7:30AM departure (yeah right! now that's starting to get a little early for me) they also have a 10:30 departure as well as their afternoon departure. Leaving mid-morning would allow me to sleep a little later yet still get to Jaco with plenty of daylight left.