Mana Khemia certainly doesn't fall short on entertainment.
The alchemy system was something I had a lot of fun with in Atelier Iris 3, and while Mana Khemia makes it more confusing and time consuming, I still liked it a great deal. The way to "level up" in the game is connected to the alchemy you've done and the amount of items synthesized. If you synth the correct items, they can be added to the "grow books" of each of your characters and awaken nodes in which you can use AP earned from battle to purchase stat boosts, new skills, etc.
This gives the game a little more of a challenge, and makes it impossible for players to overlevel. If you're having trouble in the game but have no new recipes to synth, therefore cannot upgrade your grow book... you might be in a bit of trouble. But for the most part, the game is easy, unless you decide to take on some tough fighting jobs, or venture into the bonus dungeon.
The dungeons in Mana Khemia vastly improve on Atelier Iris 3's five repetitive dungeons which you needed to return to countless times over and over again. There are too many dungeons to keep track of in MK, and extentions of dungeons so you won't quickly get bored of the scenery. This was nice in and of itself, and the methods of gathering materials for alchemy are amazing this time around. Bags, barrels and crates dot dungeons from beginning to end, plus a variety of search points where you can gather two or more of a certain ingredient such as veggies, fruits, or rocks and minerals from mining. You can also fish endlessly at fishing search points, but if you choose to do so you need to watch out for occasional monster attacks. Just to add some spice into the mix.
The battle system in MK is also very fun -- more so the more characters you have in your party. In the beginning, you're stuck with a three character party but later on you can have a party of six... three in the battle and three back up characters that you can switch in and out of battle making the battles seem more fast paced. Sometimes after attacking an enemy, you'll get a prompt for attack support, and if taken a character on standby will pop into battle and get an extra attack in for you. Defense support is also possible, where a standby character will switch with a character and half the damage taken. The whole system overall is very enjoyable, and adds some new things to the standard RPG turn-based battle system. Never a dull moment.
Now, storywise, the game follows Vayne Aurelius' three years at an alchemy school. The academy setting is a great deal of fun. You'll end up taking classes which are mostly like field trips, and striving to get an A on all assignments. Sometimes this is easy, sometimes difficult. If you manage to get the required units from all your classes, you get free time... if you get straight A's a GREAT deal of free time throughout the game. (If you don't get the required units, you end up with detention. Something I'd like to try next playthrough. ;D)
You have way more free time than courses to take, but this certainly isn't a bad thing. Your free time can be used to take jobs (collecting items for others, fighting monsters) to rack up some cash, exploring dungeons and gathering, doing some alchemy, etc. Just whatever you want to do. But the main draw to free time is the character quests you can do during each free block (or week). Talking to a character in your workshop may prompt you to hang out with them or just see what they're up to. This initiates a character quest for that character. And since Mana Khemia offers a large cast of playable characters, there's plenty of these quests to be had. Whoever you do the most character quests for will decide the ending of Mana Khemia, giving the game good replay value.
The characters themselves are quite bright, with colourful and fairly unique personalities. The cast's random chatter is filled with different events and amusing antics making them a pretty loveable bunch.
The music was definitely an improvement from Atelier Iris 3's repetitive melodies you had to listen to constantly because of the restriction of places to visit. And instead of annoying you, MK's music is a joy to listen to. Thank goodness for that.
Overall, I'd have to say Mana Khemia was an awesome game -- I enjoyed every minute of it. Though the story isn't anything special, the gameplay and characters more than make it worth a try.