Both phones launched with Android 4.4 KitKat though the Samsung Galaxy Alpha is at 4.4.4, while the HTC One mini 2 is at 4.4.2. Those are minor things, of course, the major difference in experience comes from the custom skins, TouchWiz and Sense.
TouchWiz and Sense (the latest versions of each) are quite popular, but here's a quick video anyway to get you up to speed.
In terms of looks, the two are near polar opposites but there's a fairly big cross section of matching features.
The lockscreens are different enough. Samsung has been unusually restrained and by default the Galaxy Alpha shows nothing more than the time and weather, a camera shortcut and notifications if there are any. The fingerprint scanner on the Home key can be used to secure the lockscreen instead of the usual password or pattern protection.
HTC on the other hand have kept the four shortcuts at the bottom of the screen from the early versions of Sense for Android. From here you can also launch BlinkFeed and Google Now. Unfortuantely, the double-tap to wake option from the big One (M8) is missing and you have to reach for the power key.
In case you haven't yet seen BlinkFeed - it's a magazine-like interface that shows a stream of news articles, along with updates from both social networks and apps on the device. This means BlinkFeed will show you drawings your kid made in Kid Mode, info from Fitbit workouts and so on.
Samsung recently added a similar feature called My Magazine to the homescreen. This one pulls info purely from web sites and social networks, apps can't post notifications here.
Magazines aside, the homescreens are standard with shortcuts, folders and widgets. The app drawers are pretty standard too, except on the Samsung you scroll horizontally, while on the HTC it's vertical.
The notification areas, however, are quite different. HTC uses the stock Android solution of notifications only with a button to bring up toggles (you can use a two-finger swipe for that too).
Samsung shows a row of toggles in the notification area by default, followed by S Finder and Quick connect buttons, then comes a brightness slider (with an Auto check box) and only then the notifications.
This is a little busy on a 4.7" screen so you can hide the brightness slider to free up some room, but not the S Finder and Quick connect buttons. The TouchWiz notification area can also show all toggles and has a larger number thereof overall. This includes things like NFC and Sync that can be quite useful. You can rearrange the toggles to bring the most frequently used ones forward.
Both companies couldn't resist tinkering with the app switcher UI either. Samsung has stayed close to stock with a vertical list of app thumbnails and icons (the design is slightly different from AOSP) and has added a Task manager and Close all buttons.
HTC made the bigger change and displays apps in a 3 x 3 grid of app thumbnails. This switcher lets you swipe to dismiss apps, but you can't see the 10th most recent app. There are Task manager and Close all buttons here too.
Multi Window is a serious multitasking tool exclusive to Samsung's premium line of devices. It allows you to run two apps simultaneously, so you can run two chat sessions at the same time, or a web browser for reference while writing an email or editing a document.
While Multi Window is better suited for tablets, it's still usable on the 4.7" 720p screen of the Samsung Galaxy Alpha.
Multitaskers will get a number of benefits from Samsung's interface - the readily available toggles and the ability to run two apps will save you seconds at a time, but those add up quickly over extended use.
The Galaxy Alpha also has a leg up on the HTC One mini 2 in terms of security thanks to its fingerprint scanner and the government-certified KNOX software that handles security on the phone. We already covered the lockscreen, but the Private mode can fingerprint-secure even individual files independently from the unlock routine used. This is great for keeping files private (work or personal files) while someone else is borrowing your phone.
If you work for one of the companies that let you bring your own device instead of a dedicated work phone, you'll feel a lot safer knowing private files are locked behind KNOX and a fingerprint scanner. This works equally well for sensitive company files you wouldn't want your friends to just open when borrowing your device.
The two phones have Do not disturb modes (it's called Blocking mode in TouchWiz). They can be scheduled or manually turned on and off, they block notifications and ringers except for messages and calls coming on a pre-defined shortlist.
The HTC One mini 2 offers Kids and car modes. The free Zoodles app lets kids play games, draw, read books and even check email, without getting access to the entire phone functionality and content. Then there's car mode, which gives you quick access to the music player, navigation, phone and voice commands.
Both phones feature extreme power saving modes. They disable most features, including turning off the data connection while the display is off, dimming the screen and showing a stripped down homescreen. They do this in order to last several hours per battery charge percentage point.
Winner: Samsung Galaxy Alpha. The phone caters to the increasing security concerns of users with the fingerprint lockscreen and Private mode. Mutli-window will see less use than on bigger devices, but it's there if you need it.
The HTC One mini 2 has an attractive UI (arguably prettier than TouchWiz) but not all changes are good (the app switcher, for example). The Kids and car modes are nice additions but are not enough.